Multiple platform build/check report for BioC 3.19 - CHECK results for biodbChebi on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4757
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4491
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4522
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4468
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*

CHECK results for biodbChebi on kjohnson3

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: 2024-06-10 08:51:42 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 08:54:25 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 162.7 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: aarch64-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 Ventura 13.6.5
* 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
ChebiConn 2.761  1.306   9.083
* 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-arm64/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: aarch64-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 [2024-06-10 08:53:11.720][biodb::testContext]
biodb.INFO [2024-06-10 08:53:11.727][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:53:11.732][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-10 08:53:11.733][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:53:11.734][biodb::testContext]
biodb.INFO [2024-06-10 08:53:11.751][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:53:11.754][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 08:53:11.768][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:53:11.775][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 08:53:11.777][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 08:53:11.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.788][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 08:53:11.820][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 08:53:11.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.831][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 08:53:11.833][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 08:53:11.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.842][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 08:53:11.843][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 08:53:11.847][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 08:53:11.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.879][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 08:53:11.880][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 08:53:11.881][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 08:53:11.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.884][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 08:53:11.885][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 08:53:11.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.888][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 08:53:11.889][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 08:53:11.890][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 08:53:11.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.904][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 08:53:11.905][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 08:53:11.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.912][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.DEBUG[2024-06-10 08:53:11.913][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 08:53:11.916][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 08:53:11.917][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 08:53:11.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.923][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:53:11.928][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 08:53:11.930][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 08:53:11.931][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 08:53:11.936][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 08:53:11.938][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 08:53:11.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.946][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 08:53:11.949][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 08:53:11.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.959][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 08:53:11.960][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 08:53:11.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.968][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 08:53:11.971][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 08:53:11.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.977][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 08:53:11.979][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 08:53:11.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.984][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 08:53:11.986][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 08:53:11.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:11.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:11.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:11.995][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:53:11.997][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 08:53:12.054][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 08:53:12.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.062][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 08:53:12.067][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 08:53:12.069][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 08:53:12.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.084][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 08:53:12.151][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.186][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-10 08:53:12.187][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.190][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:53:12.192][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.193][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.199][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.200][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.202][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:53:12.206][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:53:12.208][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.209][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 08:53:12.211][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:53:12.213][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.214][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.215][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:53:12.215][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:53:12.215][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:53:12.215][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:53:12.215][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:53:12.221][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:53:12.222][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:53:12.226][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:53:12.228][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:53:12.229][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:53:12.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:53:12.235][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.236][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.237][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:53:12.239][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:53:12.241][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.248][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.250][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 08:53:12.256][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.257][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:53:12.258][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.265][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:53:12.267][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.272][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.273][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.278][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.280][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:53:12.283][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:53:12.285][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.286][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 08:53:12.287][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:53:12.293][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.294][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.295][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:53:12.295][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:53:12.295][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:53:12.295][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:53:12.295][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:53:12.299][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:53:12.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:53:12.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:53:12.307][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:53:12.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:53:12.309][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:53:12.314][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.315][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.316][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:53:12.317][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:53:12.318][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.319][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.320][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 08:53:12.324][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.325][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-10 08:53:12.326][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.327][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:53:12.328][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.329][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.329][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.330][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.346][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:53:12.348][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:53:12.349][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.350][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 08:53:12.350][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:53:12.351][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.352][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.353][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.354][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:53:12.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:53:12.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:53:12.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:53:12.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:53:12.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:53:12.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.367][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.368][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:53:12.373][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:53:12.375][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.376][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.379][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 08:53:12.382][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.388][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:53:12.389][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.390][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:53:12.396][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.398][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.402][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.403][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.408][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:53:12.410][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:53:12.411][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.416][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 08:53:12.418][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:53:12.422][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.423][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.428][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.429][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:53:12.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:53:12.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:53:12.437][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:53:12.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:53:12.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:53:12.443][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.444][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.445][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:53:12.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:53:12.452][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.453][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:53:12.464][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:53:12.466][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.531][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[2024-06-10 08:53:12.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.558][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[2024-06-10 08:53:12.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.582][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[2024-06-10 08:53:12.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.604][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[2024-06-10 08:53:12.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.619][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 08:53:12.630][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 08:53:12.632][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 08:53:12.633][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 08:53:12.634][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:53:12.635][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 08:53:12.637][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 08:53:12.638][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 08:53:12.639][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 08:53:12.640][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 08:53:12.641][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:53:12.643][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 08:53:12.644][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 08:53:12.645][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 08:53:12.646][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 08:53:12.648][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 08:53:12.649][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 08:53:12.650][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 08:53:12.652][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:53:12.653][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 08:53:12.654][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 08:53:12.656][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 08:53:12.657][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 08:53:12.658][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 08:53:12.660][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 08:53:12.661][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 08:53:12.662][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 08:53:12.664][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 08:53:12.665][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 08:53:12.666][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 08:53:12.667][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 08:53:12.669][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 08:53:12.670][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 08:53:12.671][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 08:53:12.673][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 08:53:12.674][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 08:53:12.675][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 08:53:12.677][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 08:53:12.678][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 08:53:12.679][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 08:53:12.681][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 08:53:12.682][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 08:53:12.684][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 08:53:12.685][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 08:53:12.702][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 08:53:12.704][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 08:53:12.706][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 08:53:12.708][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 08:53:12.709][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 08:53:12.710][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 08:53:12.712][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 08:53:12.713][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 08:53:12.714][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 08:53:12.716][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 08:53:12.717][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 08:53:12.719][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 08:53:12.720][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 08:53:12.721][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 08:53:12.723][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 08:53:12.724][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 08:53:12.726][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 08:53:12.727][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 08:53:12.728][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 08:53:12.730][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 08:53:12.731][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 08:53:12.733][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 08:53:12.735][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:53:12.737][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:53:12.738][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 08:53:12.740][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 08:53:12.741][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 08:53:12.743][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 08:53:12.745][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 08:53:12.746][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 08:53:12.747][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 08:53:12.749][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 08:53:12.750][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 08:53:12.752][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 08:53:12.753][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 08:53:12.755][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 08:53:12.756][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 08:53:12.758][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 08:53:12.760][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 08:53:12.766][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 08:53:12.768][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:53:12.772][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:53:12.773][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.775][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.808][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[2024-06-10 08:53:12.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.813][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[2024-06-10 08:53:12.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.846][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[2024-06-10 08:53:12.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.862][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[2024-06-10 08:53:12.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:53:12.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:12.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:12.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:12.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:12.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:12.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:12.876][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-10 08:53:12.900][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-10 08:53:12.903][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.904][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.905][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.906][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:53:12.906][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.907][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.908][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.909][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-10 08:53:12.910][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-10 08:53:12.911][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:53:12.912][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.913][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-10 08:53:12.914][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-10 08:53:12.915][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-10 08:53:12.916][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 08:53:12.917][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:53:12.917][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:53:12.917][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:53:12.918][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-10 08:53:12.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:53:12.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:53:12.921][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:53:12.922][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:53:12.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:53:12.924][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:53:12.925][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:12.925][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-10 08:53:12.926][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:53:12.926][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:53:12.927][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 08:53:12.928][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-10 08:53:12.928][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-10 08:53:12.934][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:53:12.937][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:53:12.939][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-10 08:53:12.940][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:53:12.941][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:53:12.943][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:53:12.978][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-10 08:53:12.980][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-10 08:53:12.984][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-10 08:53:12.988][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-10 08:53:12.993][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 08:53:12.994][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 08:53:12.995][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-10 08:53:12.996][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-10 08:53:13.007][biodb::testThat]
biodb.INFO [2024-06-10 08:53:13.009][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-10 08:53:13.009][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:13.010][biodb::testThat]
biodb.TRACE[2024-06-10 08:53:13.016][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-06-10 08:53:13.020][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:13.027][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:13.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:13.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:13.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:13.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:13.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:13.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:13.085][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.TRACE[2024-06-10 08:53:13.099][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.101][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.103][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.136][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:13.138][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:13.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.144][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.188][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:13.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:13.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.195][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:13.199][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:13.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.202][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.205][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:13.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:13.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.242][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:13.243][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:13.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.245][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:13.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:13.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.250][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:13.251][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:13.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.252][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:13.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:13.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.257][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:13.258][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:13.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.260][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.261][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:13.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:13.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.264][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:13.265][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.267][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.268][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:13.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.271][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.272][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.274][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.279][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:13.280][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:13.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.281][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.282][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:13.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:13.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.286][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:13.287][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:13.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.288][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.290][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:13.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:13.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.293][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:13.294][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:13.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.296][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.297][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:13.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:13.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:13.374][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-06-10 08:53:13.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:13.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:13.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:13.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:13.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:13.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:13.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:13.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:13.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.484][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:53:13.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:53:13.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.487][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:53:13.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:53:13.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 08:53:13.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 08:53:13.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.494][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 08:53:13.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 08:53:13.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.671][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.675][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.678][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:13.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:13.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.756][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.757][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.762][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:13.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:13.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:13.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:13.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:13.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:13.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:13.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.795][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:13.796][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:13.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.798][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:13.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:13.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.820][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:13.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:13.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:13.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:13.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.836][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:13.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:13.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.846][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:13.848][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:13.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.854][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.856][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:13.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:13.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.894][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.895][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.899][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:13.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.946][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.947][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.949][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:13.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.962][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:13.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:13.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.966][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:13.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:13.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.970][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:13.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:13.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.988][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:13.990][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:13.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.992][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:13.993][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:13.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:13.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:13.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.005][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.009][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.013][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.017][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.018][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.019][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.020][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.044][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.051][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.059][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.067][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.069][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.072][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.077][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.100][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:14.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:14.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.109][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:14.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:14.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.117][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:14.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:14.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.125][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:14.128][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:14.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.130][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.134][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:14.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:14.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.152][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.159][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.160][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.161][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.162][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:14.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:14.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.178][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:14.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:14.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:14.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:14.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.184][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:14.185][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:14.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.187][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:14.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:14.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.208][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:14.209][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:14.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.215][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.254][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:14.255][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:14.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.259][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.268][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:14.272][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:14.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.274][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.281][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:14.285][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:14.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.287][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.301][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.303][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.307][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.318][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.321][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.325][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.336][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:14.338][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:14.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.340][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.346][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:14.348][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:14.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.350][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.357][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.359][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.361][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.367][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:14.368][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:14.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.370][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.376][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:14.377][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:14.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.379][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 08:53:14.390][biodb::testThat]
biodb.INFO [2024-06-10 08:53:14.391][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-10 08:53:14.392][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:14.393][biodb::testThat]
biodb.DEBUG[2024-06-10 08:53:14.407][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-06-10 08:53:14.415][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:14.420][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-06-10 08:53:14.421][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:14.422][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-06-10 08:53:14.424][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:14.446][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:14.448][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:14.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:14.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:14.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:14.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:14.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:14.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:14.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:14.462][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:14.464][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:14.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.465][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:14.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:14.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.502][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:14.503][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:14.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.505][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.507][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:14.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:14.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.511][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:14.512][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:14.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.514][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.515][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:14.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:14.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.520][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:14.521][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:14.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.522][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:14.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:14.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.528][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.529][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.530][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:14.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.536][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.538][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.539][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.541][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:14.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.545][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:14.546][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:14.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.548][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.549][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:14.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:14.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.553][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:14.554][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:14.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.556][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:14.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.561][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:14.562][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:14.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.564][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:14.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:14.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.569][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:14.570][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.572][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.573][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:14.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:14.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.576][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:14.577][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:14.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.579][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.580][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:14.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:14.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:14.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:14.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:14.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:14.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:14.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:14.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:14.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:14.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:14.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:14.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:14.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:14.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:14.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:14.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:14.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:14.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:14.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:14.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:14.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:14.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:14.619][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-06-10 08:53:14.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-10 08:53:14.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-10 08:53:14.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-10 08:53:14.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-10 08:53:14.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-10 08:53:14.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-10 08:53:14.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:53:14.656][biodb::testThat]
biodb.INFO [2024-06-10 08:53:14.657][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-10 08:53:14.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:14.659][biodb::testThat]
biodb.TRACE[2024-06-10 08:53:14.662][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:14.663][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:14.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.665][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:14.666][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-06-10 08:53:14.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:14.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:14.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:14.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:14.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:14.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:14.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:14.748][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-06-10 08:53:14.758][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-10 08:53:14.795][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:14.823][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-10 08:53:14.827][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:14.829][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-10 08:53:14.868][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[2024-06-10 08:53:14.876][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:14.878][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 08:53:14.880][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:14.885][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-10 08:53:14.887][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-06-10 08:53:14.945][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:14.948][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:14.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.950][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:14.953][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:14.954][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:14.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:14.959][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 08:53:14.965][biodb::testThat]
biodb.INFO [2024-06-10 08:53:14.966][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-10 08:53:14.967][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:14.968][biodb::testThat]
biodb.TRACE[2024-06-10 08:53:15.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:15.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:15.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:15.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:15.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:15.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:15.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:15.120][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[2024-06-10 08:53:15.124][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:15.127][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 08:53:15.128][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:15.130][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-06-10 08:53:15.153][biodb::testThat]
biodb.INFO [2024-06-10 08:53:15.155][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-10 08:53:15.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:15.173][biodb::testThat]
biodb.TRACE[2024-06-10 08:53:15.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:15.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:15.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:15.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:15.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:15.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:15.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:15.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:15.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:15.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:15.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:15.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:15.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.238][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:53:15.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:53:15.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.244][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:53:15.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:53:15.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.251][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 08:53:15.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 08:53:15.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.258][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 08:53:15.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 08:53:15.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:15.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:15.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:15.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:15.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.291][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:15.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:15.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:15.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:15.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:15.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:15.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:15.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:15.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.305][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:53:15.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:53:15.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.308][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 08:53:15.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 08:53:15.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.312][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 08:53:15.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 08:53:15.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:15.316][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 08:53:15.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 08:53:15.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:15.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:53:15.335][biodb::testThat]
biodb.INFO [2024-06-10 08:53:15.340][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-10 08:53:15.342][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:15.343][biodb::testThat]
biodb.INFO [2024-06-10 08:53:15.359][biodb::testThat]
biodb.INFO [2024-06-10 08:53:15.363][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-10 08:53:15.365][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:15.365][biodb::testThat]
biodb.INFO [2024-06-10 08:53:15.404][biodb::testThat]
biodb.INFO [2024-06-10 08:53:15.405][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-10 08:53:15.406][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:15.411][biodb::testThat]
biodb.DEBUG[2024-06-10 08:53:15.417][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-06-10 08:53:16.377][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-06-10 08:53:17.541][biodb::testThat]
biodb.INFO [2024-06-10 08:53:17.543][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-10 08:53:17.545][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:17.549][biodb::testThat]
biodb.DEBUG[2024-06-10 08:53:17.970][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[2024-06-10 08:53:18.389][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:18.391][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:18.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.398][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:18.399][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:18.401][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:18.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.457][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 08:53:18.462][biodb::testThat]
biodb.INFO [2024-06-10 08:53:18.463][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-10 08:53:18.464][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:18.467][biodb::testThat]
biodb.TRACE[2024-06-10 08:53:18.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:18.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:18.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:18.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:18.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:18.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:18.507][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:18.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:18.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:18.599][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[2024-06-10 08:53:18.603][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:18.604][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 08:53:18.606][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:18.608][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-10 08:53:18.692][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[2024-06-10 08:53:18.697][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:18.699][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 08:53:18.701][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:18.703][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-06-10 08:53:18.729][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 08:53:18.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 08:53:18.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:18.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:18.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:18.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:18.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:18.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:18.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:18.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:18.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:18.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:18.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:18.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:18.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:18.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:18.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:18.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:18.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:18.781][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[2024-06-10 08:53:18.787][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:18.790][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-10 08:53:18.812][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:18.819][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-10 08:53:18.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:18.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:18.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:18.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:18.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:18.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:18.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:18.848][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-06-10 08:53:18.932][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:18.935][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-06-10 08:53:18.939][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:18.940][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:18.946][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:18.948][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:18.952][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:18.954][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:18.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:18.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:18.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:18.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:18.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:18.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:18.986][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[2024-06-10 08:53:18.987][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-06-10 08:53:18.995][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:19.000][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:19.002][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-06-10 08:53:19.381][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-06-10 08:53:19.759][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:19.763][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-06-10 08:53:19.817][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-06-10 08:53:19.822][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-06-10 08:53:19.825][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:19.828][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:19.831][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:19.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:19.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:19.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:19.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:19.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:19.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:19.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:19.861][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:19.865][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:19.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.867][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:19.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:19.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.878][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:19.879][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:19.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.883][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.886][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:19.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:19.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.897][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:19.899][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:19.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.905][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.909][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:19.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:19.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.915][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:19.916][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:19.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.917][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:19.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:19.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.922][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:19.923][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:19.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.925][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:19.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:19.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.940][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:19.945][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:19.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.947][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.950][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:19.951][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:19.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.958][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.960][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:19.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:19.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.967][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:19.970][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:19.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.973][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:19.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:19.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.983][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:19.984][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:19.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.987][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.989][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:19.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:19.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.995][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:19.996][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:19.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:19.998][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:19.999][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:20.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:20.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.005][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:20.006][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:20.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.027][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:20.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:20.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:20.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:20.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:20.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:20.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:20.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:20.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:20.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:20.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:20.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:20.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:20.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:20.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:20.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:20.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:20.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:20.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:20.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:20.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:20.068][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-06-10 08:53:20.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:20.091][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[2024-06-10 08:53:20.096][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:20.099][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-10 08:53:20.100][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:20.107][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-10 08:53:20.125][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:20.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:20.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:20.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:20.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:20.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:20.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:20.138][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:20.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:20.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:20.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:20.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:20.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:20.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:20.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:20.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:20.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:20.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:20.177][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-06-10 08:53:20.179][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:20.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-06-10 08:53:20.182][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:20.183][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:20.184][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:20.185][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:20.186][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:20.187][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:20.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:20.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:20.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:20.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:20.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:20.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:20.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:20.212][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-06-10 08:53:20.226][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:20.227][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:20.249][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-06-10 08:53:20.628][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-06-10 08:53:20.999][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:21.003][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-06-10 08:53:21.012][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-06-10 08:53:21.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-06-10 08:53:21.021][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:21.047][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:21.050][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:21.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:21.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:21.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:21.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:21.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:21.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:21.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:21.078][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:21.082][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:21.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.084][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:21.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:21.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.094][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:21.097][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:21.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.100][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.105][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:21.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:21.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.110][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:21.111][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:21.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.112][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.114][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:21.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:21.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.118][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:21.119][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:21.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.121][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:21.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:21.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.126][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:21.127][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:21.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.129][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.130][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:21.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:21.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.134][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:21.135][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:21.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.137][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.138][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:21.139][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.141][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.142][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:21.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.146][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:21.147][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:21.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.149][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:21.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:21.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.156][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:21.158][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:21.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.160][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:21.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:21.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.168][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:21.170][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:21.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.174][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.176][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:21.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:21.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.180][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:21.181][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:21.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.182][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.184][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:21.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:21.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:21.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:21.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:21.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:21.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:21.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:21.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:21.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:21.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:21.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:21.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:21.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:21.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:21.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:21.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:21.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:21.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:21.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:21.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:21.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:21.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:21.249][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-06-10 08:53:21.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:21.294][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[2024-06-10 08:53:21.298][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:21.300][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 08:53:21.301][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:21.303][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-10 08:53:21.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:21.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:21.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:21.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:21.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:21.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:21.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:21.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:21.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:21.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:21.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:21.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:21.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:21.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:21.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:21.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:21.359][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:21.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:21.364][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-06-10 08:53:21.365][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:21.367][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-06-10 08:53:21.369][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:21.371][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:21.376][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:21.377][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:21.378][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:21.405][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:21.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:21.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:21.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:21.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:21.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:21.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:21.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:21.444][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-06-10 08:53:21.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:21.452][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:21.453][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-06-10 08:53:21.848][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-06-10 08:53:22.221][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:22.227][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-06-10 08:53:22.234][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-06-10 08:53:22.243][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-06-10 08:53:22.247][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:22.249][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:22.251][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:22.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:22.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:22.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:22.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:22.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:22.277][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:22.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:22.284][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:22.285][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:22.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.290][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:22.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:22.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.305][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:22.307][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:22.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.311][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.312][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:22.315][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:22.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.317][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.320][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:22.321][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:22.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.323][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.324][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:22.324][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:22.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.326][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.327][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:22.328][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:22.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.330][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.331][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:22.332][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.333][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.334][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:22.335][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:22.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.336][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.337][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:22.338][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:22.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.340][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:22.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:22.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.344][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:22.346][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:22.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.349][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.351][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:22.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:22.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.362][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:22.365][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:22.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.367][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:22.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:22.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:22.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:22.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:22.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:22.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:22.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:22.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:22.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:22.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:22.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:22.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:22.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:22.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:22.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:22.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:22.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:22.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:22.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:22.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:22.449][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-06-10 08:53:22.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:22.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:22.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:22.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:22.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:22.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:22.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:22.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:22.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:22.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:22.482][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[2024-06-10 08:53:22.483][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-06-10 08:53:22.484][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:22.486][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-06-10 08:53:22.488][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:22.490][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:22.491][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:22.492][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:22.493][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:22.494][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:22.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:22.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:22.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:22.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:22.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:22.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:22.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:22.520][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-06-10 08:53:22.527][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:22.528][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:22.529][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-06-10 08:53:22.915][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-06-10 08:53:23.298][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:23.303][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-06-10 08:53:23.312][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-06-10 08:53:23.321][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-06-10 08:53:23.325][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:23.330][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:23.332][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:23.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:23.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:23.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:23.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:23.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:23.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:23.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:23.376][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:23.377][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:23.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.379][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:23.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:23.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.386][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:23.387][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:23.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.388][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.390][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:23.391][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:23.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.393][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.394][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:23.396][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:23.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.397][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.399][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:23.400][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:23.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.401][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.402][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:23.403][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:23.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.405][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.406][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:23.407][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.409][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.410][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:23.411][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:23.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.413][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.414][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:23.415][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:23.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.417][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:23.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:23.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.422][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:23.423][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:23.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.425][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.427][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:23.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:23.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.430][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:23.431][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:23.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.433][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:23.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:23.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:23.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:23.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:23.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:23.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:23.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:23.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:23.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:23.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:23.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:23.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:23.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:23.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:23.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:23.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:23.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:23.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:23.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:23.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:23.491][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-06-10 08:53:23.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:23.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:23.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:23.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:23.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:23.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:23.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:23.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:23.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:23.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:23.535][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[2024-06-10 08:53:23.536][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-06-10 08:53:23.537][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:23.539][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-06-10 08:53:23.540][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:23.541][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:23.542][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:23.543][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:23.544][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:23.545][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:23.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:23.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:23.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:23.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:23.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:23.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:23.566][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[2024-06-10 08:53:23.568][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-06-10 08:53:23.572][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:23.574][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:23.580][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-06-10 08:53:23.972][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-06-10 08:53:24.374][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:24.379][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-06-10 08:53:24.390][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-06-10 08:53:24.400][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-06-10 08:53:24.404][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:24.406][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:24.411][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:24.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:24.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:24.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:24.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:24.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:24.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:24.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:24.445][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:24.447][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:24.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.451][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:24.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:24.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.462][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:24.464][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:24.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.470][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.472][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:24.474][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:24.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.476][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.480][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:24.482][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:24.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.486][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.488][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:24.489][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:24.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.492][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.547][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:24.549][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:24.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.553][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.554][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:24.556][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.557][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.563][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:24.565][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:24.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.569][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.571][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:24.573][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:24.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.574][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:24.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:24.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.580][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:24.580][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:24.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.582][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.583][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:24.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:24.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.588][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:24.590][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:24.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.592][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:24.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:24.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:24.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:24.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:24.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:24.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:24.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:24.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:24.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:24.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:24.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:24.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:24.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:24.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:24.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:24.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:24.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:24.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:24.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:24.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:24.638][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-06-10 08:53:24.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:24.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:24.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:24.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:24.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:24.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:24.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:24.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:24.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:24.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:24.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:24.684][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-06-10 08:53:24.686][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:24.692][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-06-10 08:53:24.693][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:24.695][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:24.718][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:24.722][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:24.724][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:24.728][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:24.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:24.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:24.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:24.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:24.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:24.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:24.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:24.755][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-06-10 08:53:24.761][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:24.762][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:24.765][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-06-10 08:53:25.154][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-06-10 08:53:25.555][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:25.562][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-06-10 08:53:25.570][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-06-10 08:53:25.577][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-06-10 08:53:25.584][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:25.588][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:25.590][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:25.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:25.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:25.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:25.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:25.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:25.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:25.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:25.625][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:25.627][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:25.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.629][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:25.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:25.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.644][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:25.645][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:25.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.651][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.653][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:25.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:25.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.665][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:25.667][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:25.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.673][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.675][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:25.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:25.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.683][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:25.688][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:25.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.690][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:25.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:25.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.703][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:25.708][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:25.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.710][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:25.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:25.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.724][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:25.725][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:25.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.730][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.732][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:25.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:25.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.744][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:25.745][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:25.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.752][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.755][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:25.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:25.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.767][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:25.769][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:25.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.774][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:25.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:25.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.826][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:25.832][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:25.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.834][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:25.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:25.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.848][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:25.850][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:25.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.856][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.857][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:25.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:25.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.867][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:25.869][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:25.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.870][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.876][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:25.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:25.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:25.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:25.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:25.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:25.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:25.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:25.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:25.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:25.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:25.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:25.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:25.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:25.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:25.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:25.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:25.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:25.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:25.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:25.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:25.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:25.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:25.955][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-06-10 08:53:25.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:25.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:25.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:25.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:25.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:25.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:25.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:25.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:25.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:25.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:25.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:25.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:25.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:25.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:25.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:26.002][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[2024-06-10 08:53:26.004][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-06-10 08:53:26.005][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:26.009][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-06-10 08:53:26.011][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:26.016][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:26.018][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:26.019][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:26.025][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:26.027][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:26.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:26.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:26.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:26.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:26.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:26.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:26.077][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.DEBUG[2024-06-10 08:53:26.081][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-06-10 08:53:26.088][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:26.089][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:26.094][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-06-10 08:53:26.489][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-06-10 08:53:26.880][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:26.886][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-06-10 08:53:26.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-06-10 08:53:26.901][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-06-10 08:53:26.908][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:26.913][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:26.914][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:26.918][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:26.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:26.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:26.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:26.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:26.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:26.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:26.949][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:26.950][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:26.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:26.956][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:26.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:26.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:26.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:26.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:26.970][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:26.972][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:26.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:26.974][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:26.977][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:26.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:26.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:26.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:26.986][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:26.987][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:26.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:26.993][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:26.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:26.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:27.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.006][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:27.008][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:27.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.015][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:27.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:27.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.029][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:27.030][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:27.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.035][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.037][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:27.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:27.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.044][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:27.050][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:27.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.052][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.056][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:27.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:27.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.064][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:27.065][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:27.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.071][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.072][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:27.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:27.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.082][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:27.085][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:27.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.087][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:27.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:27.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.100][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:27.101][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:27.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.103][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:27.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:27.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.117][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:27.118][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:27.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.158][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.165][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:27.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:27.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.175][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:27.180][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:27.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.183][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.189][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:27.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:27.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:27.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:27.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:27.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:27.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:27.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:27.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:27.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:27.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:27.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:27.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:27.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:27.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:27.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:27.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:27.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:27.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:27.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:27.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:27.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:27.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:27.282][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-06-10 08:53:27.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:27.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:27.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:27.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:27.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:27.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:27.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:27.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:27.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:27.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:27.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:27.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:27.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:27.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:27.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:27.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:27.335][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-06-10 08:53:27.336][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:27.341][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-06-10 08:53:27.343][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:27.348][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:27.350][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:27.351][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:27.355][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:27.356][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:27.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:27.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:27.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:27.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:27.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:27.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:27.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:27.401][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-06-10 08:53:27.408][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:27.409][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:27.414][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-06-10 08:53:27.809][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-06-10 08:53:28.190][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:28.196][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-06-10 08:53:28.245][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-06-10 08:53:28.255][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-06-10 08:53:28.259][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:28.267][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:28.269][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:28.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:28.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:28.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:28.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:28.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:28.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:28.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:28.303][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:28.304][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:28.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.310][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:28.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:28.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.323][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:28.325][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:28.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.331][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.333][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:28.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:28.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.340][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:28.345][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:28.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.348][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.352][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:28.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:28.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.362][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:28.363][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:28.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.369][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:28.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:28.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.381][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:28.383][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:28.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.390][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:28.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:28.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.399][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:28.400][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:28.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.406][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.408][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:28.411][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:28.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.414][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.419][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:28.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:28.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.428][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:28.433][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:28.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.435][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:28.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:28.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.449][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:28.450][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:28.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.456][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:28.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:28.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.469][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:28.471][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:28.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.477][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.478][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:28.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:28.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.487][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:28.492][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:28.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.494][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.499][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:28.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:28.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:28.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:28.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:28.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:28.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:28.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:28.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:28.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:28.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:28.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:28.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:28.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:28.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:28.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:28.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:28.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:28.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:28.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:28.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:28.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:28.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:28.614][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-06-10 08:53:28.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:28.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:28.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:28.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:28.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:28.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:28.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:28.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:28.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:28.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:28.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:28.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:28.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:28.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:28.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:28.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:28.649][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-06-10 08:53:28.650][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:28.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-06-10 08:53:28.654][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:28.655][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:28.656][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:28.657][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:28.658][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:28.659][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:28.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:28.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:28.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:28.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:28.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:28.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:28.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:28.674][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-06-10 08:53:28.678][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:28.679][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:28.680][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-06-10 08:53:29.062][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-06-10 08:53:29.440][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:29.445][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-06-10 08:53:29.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-06-10 08:53:29.461][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-06-10 08:53:29.465][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:29.469][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:29.470][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:29.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:29.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:29.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:29.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:29.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:29.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:29.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:29.513][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:29.515][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:29.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.516][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:29.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:29.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.522][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:29.523][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:29.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.525][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.526][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:29.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:29.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.531][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:29.532][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:29.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.534][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.535][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:29.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:29.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.539][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:29.540][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:29.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.542][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:29.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:29.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.547][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:29.548][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:29.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.550][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:29.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:29.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.555][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:29.556][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:29.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.558][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.559][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:29.560][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:29.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.562][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.563][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:29.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:29.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.567][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:29.568][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:29.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.569][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:29.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.574][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:29.575][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:29.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.577][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:29.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:29.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.582][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:29.583][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:29.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.585][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.586][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:29.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:29.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.590][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:29.591][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:29.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.592][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.593][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:29.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:29.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:29.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:29.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:29.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:29.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:29.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:29.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:29.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:29.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:29.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:29.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:29.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:29.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:29.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:29.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:29.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:29.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:29.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:29.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:29.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:29.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:29.646][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-06-10 08:53:29.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:29.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:29.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:29.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:29.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:29.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:29.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:29.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:29.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:29.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:29.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:29.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:29.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:29.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:29.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:29.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:29.669][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-06-10 08:53:29.670][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:29.672][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-06-10 08:53:29.674][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:29.675][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:29.676][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:29.677][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:29.678][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:29.679][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:29.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:29.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:29.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:29.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:29.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:29.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:29.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:29.693][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-06-10 08:53:29.696][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:29.697][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:29.698][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-06-10 08:53:30.070][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-06-10 08:53:30.449][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:30.454][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-06-10 08:53:30.464][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-06-10 08:53:30.467][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-06-10 08:53:30.470][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:30.472][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:30.474][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:30.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:30.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:30.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:30.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:30.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:30.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:30.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:30.495][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:30.500][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:30.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.503][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:30.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:30.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.510][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:30.511][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:30.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.515][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.517][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:30.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:30.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.554][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:30.556][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:30.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.558][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.560][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:30.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:30.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.568][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:30.569][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:30.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.571][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:30.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:30.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.577][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:30.579][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:30.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.581][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:30.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:30.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.589][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:30.591][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:30.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.594][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.595][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:30.597][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:30.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.601][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.603][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:30.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:30.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.611][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:30.612][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:30.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.616][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:30.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:30.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.626][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:30.628][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:30.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.630][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:30.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:30.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.636][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:30.638][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:30.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.639][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.641][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:30.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:30.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.647][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:30.649][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:30.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.651][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.652][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:30.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:30.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:30.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:30.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:30.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:30.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:30.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:30.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:30.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:30.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:30.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:30.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:30.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:30.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:30.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:30.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:30.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:30.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:30.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:30.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:30.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:30.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:30.714][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-06-10 08:53:30.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:30.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:30.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:30.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:30.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:30.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:30.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:30.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:30.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:30.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:30.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:30.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:30.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:30.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:30.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:30.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:30.740][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-06-10 08:53:30.742][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:30.744][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-06-10 08:53:30.746][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:30.748][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:30.749][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:30.750][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:30.751][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:30.752][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:30.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:30.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:30.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:30.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:30.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:30.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:30.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:30.769][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-06-10 08:53:30.774][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:30.776][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:30.779][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-06-10 08:53:31.147][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-06-10 08:53:31.523][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:31.529][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-06-10 08:53:31.538][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-06-10 08:53:31.544][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-06-10 08:53:31.546][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:31.551][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:31.553][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:31.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:31.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:31.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:31.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:31.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:31.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:31.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:31.580][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:31.582][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:31.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.589][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:31.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.599][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:31.601][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:31.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.604][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.609][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:31.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:31.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.615][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:31.617][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:31.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.622][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.624][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:31.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:31.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.630][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:31.634][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:31.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.636][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:31.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:31.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.683][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:31.685][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:31.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.690][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:31.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:31.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.697][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:31.701][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:31.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.703][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.707][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:31.708][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:31.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.713][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.716][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:31.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:31.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.721][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:31.725][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:31.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.729][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:31.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:31.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.736][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:31.739][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:31.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.741][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:31.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:31.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.752][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:31.753][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:31.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.756][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.757][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:31.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:31.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.765][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:31.768][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:31.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.770][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.772][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:31.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:31.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:31.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:31.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:31.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:31.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:31.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:31.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:31.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:31.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:31.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:31.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:31.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:31.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:31.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:31.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:31.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:31.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:31.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:31.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:31.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:31.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:31.847][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-06-10 08:53:31.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:31.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:31.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:31.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:31.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:31.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:31.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:31.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:31.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:31.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:31.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:31.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:31.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:31.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:31.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:31.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:31.912][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-06-10 08:53:31.913][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:31.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-06-10 08:53:31.919][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:31.920][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:31.923][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:31.925][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:31.926][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:31.930][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:31.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:31.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:31.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:31.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:31.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:31.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:31.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:31.955][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-06-10 08:53:31.961][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:31.962][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:31.966][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-06-10 08:53:32.364][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-06-10 08:53:32.729][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:32.735][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-06-10 08:53:32.742][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-06-10 08:53:32.748][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-06-10 08:53:32.753][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:32.754][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:32.758][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:32.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:32.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:32.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:32.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:32.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:32.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:32.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:32.788][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:32.789][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:32.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.791][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:32.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:32.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.802][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:32.803][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:32.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.807][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.808][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:32.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:32.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.815][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:32.816][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:32.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.821][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.822][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:32.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:32.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.831][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:32.833][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:32.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.839][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.841][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:32.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:32.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.851][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:32.853][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:32.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.855][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.857][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:32.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:32.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.867][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:32.869][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:32.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.907][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.914][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:32.916][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:32.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.920][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.926][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:32.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:32.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.935][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:32.936][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:32.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.940][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:32.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:32.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.951][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:32.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:32.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.959][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:32.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:32.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.972][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:32.973][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:32.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.980][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.982][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:32.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:32.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:32.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:32.993][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:32.995][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:32.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.001][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.003][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:33.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:33.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:33.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:33.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:33.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:33.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:33.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:33.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:33.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:33.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:33.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:33.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:33.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:33.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:33.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:33.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:33.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:33.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:33.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:33.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:33.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:33.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:33.092][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-06-10 08:53:33.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:33.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:33.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:33.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:33.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:33.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:33.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:33.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:33.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:33.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:33.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:33.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:33.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:33.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:33.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:33.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:33.137][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-06-10 08:53:33.139][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:33.169][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-06-10 08:53:33.172][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:33.178][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:33.179][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:33.182][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:33.183][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:33.186][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:33.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:33.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:33.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:33.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:33.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:33.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:33.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:33.211][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-06-10 08:53:33.216][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:33.217][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:33.219][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-06-10 08:53:33.601][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-06-10 08:53:33.978][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:33.986][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-06-10 08:53:33.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-06-10 08:53:34.002][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-06-10 08:53:34.013][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:34.015][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:34.016][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:34.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:34.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:34.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:34.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:34.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:34.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:34.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:34.053][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:34.054][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:34.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.061][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:34.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:34.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.068][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:34.073][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:34.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.075][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.081][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:34.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:34.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.090][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:34.095][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:34.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.097][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.098][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:34.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:34.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.106][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:34.107][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:34.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.109][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.114][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:34.115][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:34.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.119][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.120][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:34.121][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:34.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.126][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.127][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:34.128][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:34.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.130][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.131][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:34.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:34.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.139][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:34.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:34.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.143][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:34.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:34.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.153][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:34.155][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:34.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.156][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:34.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:34.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.199][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:34.201][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:34.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.203][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.208][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:34.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:34.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.212][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:34.214][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:34.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.216][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:34.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:34.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:34.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:34.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:34.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:34.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:34.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:34.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:34.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:34.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:34.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:34.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:34.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:34.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:34.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:34.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:34.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:34.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:34.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:34.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:34.280][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-06-10 08:53:34.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:34.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:34.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:34.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:34.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:34.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:34.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:34.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:34.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:34.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:34.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:34.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:34.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:34.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:34.321][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:34.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:34.325][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-06-10 08:53:34.326][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:34.330][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-06-10 08:53:34.331][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:34.332][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:34.336][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:34.337][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:34.338][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:34.338][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:34.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:34.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:34.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:34.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:34.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:34.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:34.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:34.362][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-06-10 08:53:34.368][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:34.370][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:34.372][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-06-10 08:53:34.785][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-06-10 08:53:35.182][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:35.189][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-06-10 08:53:35.199][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-06-10 08:53:35.207][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-06-10 08:53:35.211][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:35.213][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:35.218][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:35.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:35.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:35.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:35.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:35.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:35.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:35.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:35.248][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:35.250][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:35.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.253][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:35.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:35.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.261][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:35.262][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:35.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.264][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.265][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:35.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:35.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.269][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:35.270][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:35.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.272][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.273][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:35.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:35.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.280][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:35.281][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:35.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.286][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.288][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:35.291][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:35.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.293][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.298][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:35.299][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:35.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.303][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.305][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:35.306][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:35.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.311][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.315][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:35.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:35.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.325][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:35.326][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:35.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.332][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:35.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:35.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.342][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:35.343][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:35.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.345][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.346][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:35.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:35.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.350][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:35.351][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:35.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.353][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.354][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:35.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:35.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.358][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:35.359][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:35.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.361][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:35.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:35.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:35.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:35.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:35.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:35.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:35.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:35.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:35.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:35.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:35.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:35.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:35.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:35.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:35.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:35.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:35.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:35.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:35.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:35.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:35.422][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-06-10 08:53:35.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:35.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:35.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:35.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:35.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:35.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:35.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:35.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:35.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:35.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:35.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:35.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:35.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:35.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:35.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:35.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:35.448][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-06-10 08:53:35.449][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:35.451][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-06-10 08:53:35.452][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:35.453][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:35.454][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:35.455][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:35.457][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:35.458][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:35.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:35.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:35.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:35.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:35.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:35.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:35.472][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[2024-06-10 08:53:35.473][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-06-10 08:53:35.477][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:35.478][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:35.480][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-06-10 08:53:35.891][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-06-10 08:53:36.281][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:36.288][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-06-10 08:53:36.295][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-06-10 08:53:36.303][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-06-10 08:53:36.308][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:36.309][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:36.316][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:36.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:36.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:36.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:36.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:36.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:36.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:36.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:36.376][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:36.390][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:36.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.399][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:36.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:36.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.412][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:36.414][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:36.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.418][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.420][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:36.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:36.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.429][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:36.430][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:36.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.436][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:36.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:36.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.445][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:36.449][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:36.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.451][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:36.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:36.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.466][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:36.467][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:36.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.473][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:36.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:36.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.480][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:36.485][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:36.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.487][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.492][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:36.494][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:36.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.496][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.501][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:36.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:36.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.510][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:36.511][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:36.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.516][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:36.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:36.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.524][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:36.529][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:36.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.531][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:36.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:36.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.543][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:36.544][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:36.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.550][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.552][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:36.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:36.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.560][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:36.561][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:36.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.567][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:36.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:36.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:36.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:36.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:36.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:36.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:36.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:36.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:36.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:36.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:36.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:36.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:36.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:36.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:36.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:36.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:36.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:36.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:36.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:36.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:36.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:36.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:36.641][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-06-10 08:53:36.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:36.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:36.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:36.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:36.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:36.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:36.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:36.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:36.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:36.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:36.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:36.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:36.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:36.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:36.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:36.663][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[2024-06-10 08:53:36.664][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-06-10 08:53:36.665][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:36.666][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-06-10 08:53:36.668][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:36.669][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:36.669][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:36.670][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:36.671][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:36.672][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:36.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:36.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:36.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:36.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:36.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:36.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:36.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:36.688][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-06-10 08:53:36.691][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:36.692][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:36.693][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-06-10 08:53:37.074][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-06-10 08:53:37.469][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:37.475][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-06-10 08:53:37.483][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-06-10 08:53:37.487][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-06-10 08:53:37.494][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:37.500][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:37.502][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:37.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:37.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:37.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:37.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:37.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:37.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:37.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:37.531][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:37.533][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:37.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.538][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:37.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:37.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.547][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:37.550][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:37.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.553][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.589][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:37.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:37.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.602][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:37.605][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:37.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.608][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.612][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:37.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:37.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.621][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:37.622][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:37.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.627][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:37.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:37.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.638][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:37.641][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:37.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.644][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:37.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:37.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.656][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:37.657][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:37.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.662][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.664][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:37.667][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:37.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.669][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.675][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:37.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:37.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.681][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:37.683][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:37.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.687][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:37.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:37.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.700][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:37.705][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:37.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.709][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:37.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:37.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.719][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:37.724][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:37.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.727][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.732][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:37.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:37.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.741][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:37.742][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:37.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.747][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.751][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:37.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:37.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:37.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:37.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:37.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:37.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:37.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:37.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:37.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:37.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:37.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:37.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:37.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:37.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:37.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:37.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:37.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:37.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:37.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:37.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:37.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:37.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:37.891][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-06-10 08:53:37.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:37.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:37.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:37.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:37.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:37.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:37.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:37.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:37.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:37.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:37.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:37.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:37.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:37.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:37.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:37.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:37.952][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-06-10 08:53:37.954][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:37.961][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-06-10 08:53:37.963][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:37.967][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:37.969][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:37.970][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:37.974][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:37.975][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:37.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:37.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:37.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:37.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:38.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:38.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:38.007][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[2024-06-10 08:53:38.012][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-06-10 08:53:38.018][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:38.020][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:38.026][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-06-10 08:53:38.431][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-06-10 08:53:38.809][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:38.814][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-06-10 08:53:38.819][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-06-10 08:53:38.823][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-06-10 08:53:38.826][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:38.827][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:38.829][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:38.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:38.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:38.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:38.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:38.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:38.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:38.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:38.845][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:38.846][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:38.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.849][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:38.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:38.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.854][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:38.855][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:38.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.856][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.858][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:38.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:38.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.861][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:38.862][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:38.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.864][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.865][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:38.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:38.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.869][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:38.885][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:38.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.896][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:38.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:38.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.904][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:38.905][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:38.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.907][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.908][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:38.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:38.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.912][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:38.913][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:38.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.916][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.917][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:38.919][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:38.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.921][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.922][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:38.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:38.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.926][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:38.927][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:38.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.929][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:38.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:38.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.934][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:38.935][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:38.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.936][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:38.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:38.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.942][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:38.944][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:38.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.946][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.948][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:38.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:38.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.954][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:38.955][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:38.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.957][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.959][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:38.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:38.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:38.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:38.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:38.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:38.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:38.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:38.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:38.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:38.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:38.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:38.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:38.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:38.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:38.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:38.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:38.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:38.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:39.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:39.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:39.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:39.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:39.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:39.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:39.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:39.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:39.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:39.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:39.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:39.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:39.011][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-06-10 08:53:39.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:39.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:39.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:39.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:39.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:39.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:39.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:39.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:39.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:39.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:39.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:39.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:39.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:39.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:39.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:39.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:39.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:39.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:39.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:39.051][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-06-10 08:53:39.052][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:39.053][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-06-10 08:53:39.055][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:39.056][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:39.056][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:39.057][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:39.058][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:39.059][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:39.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:39.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:39.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:39.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:39.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:39.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:39.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:39.072][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-06-10 08:53:39.075][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:39.076][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:39.078][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-06-10 08:53:39.908][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-06-10 08:53:40.283][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:40.286][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-06-10 08:53:40.293][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-06-10 08:53:40.298][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-06-10 08:53:40.301][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:40.303][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:40.306][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:40.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:40.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:40.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:40.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:40.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:40.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:40.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:40.328][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:40.329][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:40.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.331][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:40.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:40.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.335][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:40.336][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:40.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.339][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.341][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:40.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:40.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.344][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:40.345][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:40.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.346][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.347][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:40.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:40.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.351][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:40.351][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:40.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.353][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:40.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:40.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.357][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:40.358][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:40.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.360][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:40.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:40.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.386][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:40.388][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:40.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.392][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.394][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:40.395][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:40.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.397][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.398][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:40.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:40.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.402][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:40.403][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:40.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.405][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:40.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:40.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.409][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:40.410][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:40.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.412][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:40.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:40.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.419][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:40.420][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:40.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.422][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.424][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:40.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:40.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.428][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:40.429][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:40.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.431][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.432][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:40.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:40.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:40.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:40.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:40.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:40.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:40.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:40.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:40.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:40.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:40.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:40.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:40.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:40.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:40.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:40.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:40.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:40.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:40.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:40.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:40.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:40.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:40.473][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-06-10 08:53:40.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:40.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:40.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:40.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:40.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:40.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:40.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:40.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:40.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:40.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:40.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:40.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:40.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:40.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:40.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:40.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:40.518][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-06-10 08:53:40.520][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:40.523][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-06-10 08:53:40.525][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:40.526][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:40.528][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:40.528][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:40.529][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:40.530][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:40.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:40.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:40.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:40.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:40.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:40.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:40.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:40.546][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-06-10 08:53:40.549][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:40.551][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:40.552][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-06-10 08:53:40.945][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-06-10 08:53:41.303][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:41.307][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-06-10 08:53:41.312][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-06-10 08:53:41.316][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-06-10 08:53:41.318][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:41.320][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:41.321][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:41.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:41.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:41.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:41.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:41.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:41.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:41.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:41.337][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:41.339][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:41.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.341][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:41.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:41.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.346][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:41.347][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:41.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.349][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.350][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:41.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:41.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.354][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:41.354][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:41.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.356][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.358][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:41.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:41.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.361][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:41.362][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:41.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.363][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:41.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:41.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.368][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:41.368][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:41.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.370][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:41.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:41.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.374][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:41.375][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:41.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.376][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.377][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:41.378][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:41.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.379][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.380][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:41.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:41.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.384][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:41.384][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:41.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.407][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:41.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:41.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.416][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:41.418][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:41.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.422][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:41.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:41.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.427][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:41.429][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:41.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.431][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.432][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:41.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:41.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.436][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:41.438][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:41.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.439][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.440][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:41.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:41.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:41.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:41.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:41.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:41.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:41.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:41.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:41.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:41.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:41.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:41.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:41.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:41.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:41.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:41.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:41.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:41.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:41.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:41.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:41.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:41.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:41.488][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-06-10 08:53:41.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:41.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:41.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:41.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:41.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:41.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:41.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:41.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:41.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:41.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:41.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:41.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:41.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:41.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:41.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:41.516][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[2024-06-10 08:53:41.517][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-06-10 08:53:41.518][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:41.519][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-06-10 08:53:41.521][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:41.522][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:41.523][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:41.524][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:41.525][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:41.526][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:41.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:41.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:41.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:41.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:41.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:41.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:41.561][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[2024-06-10 08:53:41.563][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-06-10 08:53:41.566][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:41.567][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:41.569][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-06-10 08:53:41.931][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-06-10 08:53:42.293][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:42.297][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-06-10 08:53:42.303][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-06-10 08:53:42.307][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-06-10 08:53:42.310][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:42.312][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:42.313][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:42.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:42.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:42.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:42.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:42.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:42.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:42.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:42.333][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:42.335][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:42.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.337][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:42.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:42.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.345][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:42.347][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:42.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.350][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.352][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:42.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:42.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.359][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:42.361][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:42.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.363][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:42.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:42.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.372][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:42.374][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:42.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.377][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:42.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:42.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.388][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:42.390][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:42.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.394][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:42.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:42.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.401][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:42.403][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:42.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.405][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.407][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:42.408][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:42.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.410][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.411][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:42.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:42.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.416][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:42.418][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:42.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.422][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:42.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:42.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.428][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:42.429][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:42.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.431][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:42.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:42.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.463][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:42.465][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:42.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.469][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.470][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:42.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:42.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.475][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:42.476][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:42.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.478][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.480][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:42.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:42.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:42.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:42.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:42.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:42.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:42.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:42.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:42.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:42.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:42.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:42.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:42.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:42.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:42.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:42.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:42.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:42.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:42.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:42.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:42.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:42.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:42.525][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-06-10 08:53:42.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:42.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:42.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:42.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:42.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:42.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:42.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:42.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:42.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:42.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:42.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:42.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:42.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:42.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:42.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:42.551][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[2024-06-10 08:53:42.552][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-06-10 08:53:42.553][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:42.555][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-06-10 08:53:42.556][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:42.557][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:42.558][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:42.559][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:42.560][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:42.562][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:42.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:42.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:42.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:42.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:42.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:42.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:42.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:42.577][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-06-10 08:53:42.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:42.581][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:42.598][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-06-10 08:53:42.965][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-06-10 08:53:43.332][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:43.336][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-06-10 08:53:43.341][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-06-10 08:53:43.345][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-06-10 08:53:43.347][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:43.349][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:43.351][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:43.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:43.371][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:43.372][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:43.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.375][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:43.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:43.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.382][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:43.383][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:43.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.385][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.387][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:43.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:43.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.391][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:43.392][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:43.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.393][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.395][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:43.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:43.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.400][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:43.404][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:43.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.407][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:43.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:43.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.415][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:43.418][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:43.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.420][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:43.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:43.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.431][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:43.432][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:43.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.434][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.438][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:43.439][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.441][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.442][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:43.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.448][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:43.449][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:43.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.452][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:43.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:43.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.459][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:43.460][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:43.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.463][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:43.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:43.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.467][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:43.468][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:43.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.471][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.472][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:43.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:43.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.479][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:43.480][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:43.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.505][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.508][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:43.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:43.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:43.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:43.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:43.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:43.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:43.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:43.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:43.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:43.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:43.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:43.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:43.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:43.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:43.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:43.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:43.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:43.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:43.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:43.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:43.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:43.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.563][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-06-10 08:53:43.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.605][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[2024-06-10 08:53:43.609][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:43.611][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 08:53:43.614][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:43.616][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-10 08:53:43.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:43.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.671][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.TRACE[2024-06-10 08:53:43.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:43.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.723][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[2024-06-10 08:53:43.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:43.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:43.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:43.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.828][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[2024-06-10 08:53:43.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.848][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[2024-06-10 08:53:43.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:43.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:43.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:43.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:43.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:43.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:43.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:43.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:43.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:43.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:43.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:43.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:43.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:43.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:43.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:44.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:44.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:44.002][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[2024-06-10 08:53:44.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:44.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:44.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:44.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:44.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:44.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:44.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:44.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:44.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:44.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:44.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:44.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:44.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:44.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:44.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:44.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:44.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:44.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:44.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:44.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:44.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:44.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:44.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:44.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:44.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:44.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:44.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:44.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:44.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:44.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:44.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:44.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:44.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:44.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:44.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:44.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:44.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:44.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:44.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:44.184][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[2024-06-10 08:53:44.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:44.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:44.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:44.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:44.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:44.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:44.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:44.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:44.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:44.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:44.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:44.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:44.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:44.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:44.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:44.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:44.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:44.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:44.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:44.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:44.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:44.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:44.344][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[2024-06-10 08:53:44.348][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:44.352][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:44.354][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-10 08:53:44.725][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-10 08:53:45.088][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-06-10 08:53:45.093][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-10 08:53:45.100][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-06-10 08:53:45.106][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-06-10 08:53:45.116][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[2024-06-10 08:53:45.125][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:45.126][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:45.129][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-10 08:53:45.523][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-10 08:53:45.951][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:45.960][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-06-10 08:53:45.972][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-06-10 08:53:45.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:45.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:45.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:45.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:45.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:45.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:45.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:46.003][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-06-10 08:53:46.004][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:46.005][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-06-10 08:53:46.009][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:46.011][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:46.016][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:46.017][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:46.018][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:46.022][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:46.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:46.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:46.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:46.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:46.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:46.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:46.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:46.050][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-06-10 08:53:46.056][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:46.060][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:46.061][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-06-10 08:53:46.427][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-06-10 08:53:46.794][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:46.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-06-10 08:53:46.804][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-06-10 08:53:46.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-06-10 08:53:46.814][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:46.816][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:46.817][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:46.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:46.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:46.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:46.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:46.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:46.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:46.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:46.833][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:46.834][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:46.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.836][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:46.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:46.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.840][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:46.841][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:46.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.842][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.843][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:46.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:46.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.846][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:46.847][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:46.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.849][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:46.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:46.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.853][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:46.854][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:46.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.855][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:46.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:46.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.859][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:46.860][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:46.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.861][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:46.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:46.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.891][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:46.892][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:46.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.893][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.894][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:46.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:46.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.898][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:46.899][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:46.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.900][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.901][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:46.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:46.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.905][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:46.906][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:46.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.907][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:46.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:46.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.912][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:46.913][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:46.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.915][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.916][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:46.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:46.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.920][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:46.921][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:46.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.923][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.925][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:46.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:46.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.929][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:46.930][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:46.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.931][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.933][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:46.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:46.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:46.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:46.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:46.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:46.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:46.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:46.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:46.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:46.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:46.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:46.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:46.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:46.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:46.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:46.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:46.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:46.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:46.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:46.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:46.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:46.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:46.971][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-06-10 08:53:46.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:46.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:46.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:46.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:46.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:46.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:46.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:46.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:46.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:46.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:46.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:47.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:47.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:47.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:47.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:47.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:47.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:47.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:47.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:47.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:47.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:47.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:47.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:47.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:47.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:47.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:47.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:47.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:47.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:47.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:47.031][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-06-10 08:53:47.032][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:47.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-06-10 08:53:47.035][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:47.036][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:47.037][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:47.038][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:47.039][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:47.040][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:47.043][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:47.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:47.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:47.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:47.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:47.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:47.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:47.054][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-06-10 08:53:47.057][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:47.058][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:47.059][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-06-10 08:53:47.443][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-06-10 08:53:47.815][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-06-10 08:53:47.819][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-10 08:53:47.822][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-06-10 08:53:47.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-06-10 08:53:47.837][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-06-10 08:53:47.843][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:47.845][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:47.847][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:47.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:47.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:47.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:47.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:47.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:47.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:47.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:47.866][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:47.867][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:47.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.869][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:47.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:47.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.874][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:47.875][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:47.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.877][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.878][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:47.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:47.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.881][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:47.882][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:47.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.906][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.909][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:47.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:47.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.916][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:47.917][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:47.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.919][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.921][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:47.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:47.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.924][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:47.925][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:47.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.927][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:47.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:47.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.933][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:47.934][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:47.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.936][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.937][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:47.938][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:47.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.940][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.942][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:47.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:47.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.946][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:47.947][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:47.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.949][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:47.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:47.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.954][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:47.955][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:47.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.957][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:47.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:47.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.962][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:47.963][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:47.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.965][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.967][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:47.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:47.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.972][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:47.973][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:47.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.975][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.977][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:47.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:47.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:47.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:47.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:47.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:47.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:47.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:47.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:47.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:47.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:47.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:47.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:47.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:47.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:47.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:48.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:48.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:48.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:48.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:48.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:48.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:48.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:48.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:48.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:48.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:48.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:48.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:48.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:48.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:48.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:48.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:48.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:48.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:48.031][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-06-10 08:53:48.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:48.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:48.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:48.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:48.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:48.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:48.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:48.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:48.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:48.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:48.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:48.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:48.069][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[2024-06-10 08:53:48.073][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:48.075][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:48.077][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-10 08:53:48.602][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-10 08:53:49.155][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:49.161][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-10 08:53:49.171][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-10 08:53:49.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:49.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:49.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:49.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:49.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:49.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:49.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:49.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:49.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:49.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:49.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:49.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:49.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:49.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:49.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:49.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:49.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:49.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:49.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:49.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:49.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:49.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:49.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:49.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:49.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:49.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:49.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:49.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:49.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:49.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:49.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:49.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:49.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:49.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:49.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:49.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:49.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:49.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:49.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:49.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:49.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:49.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:49.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:49.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:49.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:49.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:49.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:49.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:49.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:49.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:49.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:49.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:49.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:49.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.565][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.615][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.675][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:50.679][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:50.681][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 08:53:50.683][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:50.685][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-10 08:53:50.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.760][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.828][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:50.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:50.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:50.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:50.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:50.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:50.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:50.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:50.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:50.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:50.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:50.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:51.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:51.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:51.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:51.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:51.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:51.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:51.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:51.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:51.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:51.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:51.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.350][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 08:53:51.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 08:53:51.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:53:51.366][biodb::testThat]
biodb.INFO [2024-06-10 08:53:51.367][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-10 08:53:51.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:51.369][biodb::testThat]
biodb.TRACE[2024-06-10 08:53:51.374][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 08:53:51.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 08:53:51.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:51.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:51.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:51.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:51.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:51.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:51.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:51.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:51.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:51.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:51.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:51.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:51.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:51.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:51.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:51.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:51.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:51.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:51.415][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:51.419][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:51.420][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:51.422][private$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[2024-06-10 08:53:51.813][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[2024-06-10 08:53:52.191][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:52.197][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-10 08:53:52.207][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-10 08:53:52.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:52.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:52.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:52.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:52.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:52.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:52.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:52.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:52.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:52.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:52.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:52.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:52.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:52.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:52.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:52.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:52.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:52.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:52.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:52.278][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[2024-06-10 08:53:52.284][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:52.289][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:52.292][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-10 08:53:52.672][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-10 08:53:53.038][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:53.044][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-10 08:53:53.054][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-10 08:53:53.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:53.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:53.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:53.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:53.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:53.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:53.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:53.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:53.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:53.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:53.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:53.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:53.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:53.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:53.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:53.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:53.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:53.116][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 08:53:53.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:53.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:53.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:53.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:53.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:53.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:53.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:53.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.139][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.140][private$selectFields]
biodb.TRACE[2024-06-10 08:53:53.141][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:53.142][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:53.143][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.144][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.145][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.147][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.148][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.149][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.151][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.152][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.153][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.154][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.155][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.156][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.157][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:53.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.179][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-10 08:53:53.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:53.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:53.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:53.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:53.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:53.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:53.215][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.TRACE[2024-06-10 08:53:53.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.225][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.226][private$selectFields]
biodb.TRACE[2024-06-10 08:53:53.227][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:53.228][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:53.229][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.232][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.236][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.237][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.238][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.240][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.242][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.243][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:53.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.256][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 08:53:53.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:53.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:53.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:53.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:53.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:53.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:53.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:53.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.278][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.279][private$selectFields]
biodb.TRACE[2024-06-10 08:53:53.280][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:53.281][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:53.282][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.283][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.284][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.286][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.287][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.288][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.289][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.290][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.291][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:53.292][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.293][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.295][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.296][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:53.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:53.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.310][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-10 08:53:53.311][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 08:53:53.312][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 08:53:53.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:53.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:53.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:53.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:53.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:53.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:53.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:53.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:53.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:53.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:53.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:53.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:53.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:53.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:53.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:53.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:53.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:53.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:53.410][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:53.414][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:53.415][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:53.418][private$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[2024-06-10 08:53:53.801][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[2024-06-10 08:53:54.178][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:54.182][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-06-10 08:53:54.193][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-06-10 08:53:54.200][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[2024-06-10 08:53:54.209][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:54.210][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:54.212][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-10 08:53:54.602][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-10 08:53:54.994][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:55.000][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-06-10 08:53:55.012][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-06-10 08:53:55.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.174][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 08:53:55.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.298][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.299][private$selectFields]
biodb.TRACE[2024-06-10 08:53:55.300][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:55.302][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:55.304][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.306][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.312][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.314][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.319][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.320][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.325][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.326][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.327][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.328][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.334][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.336][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.340][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:55.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.371][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-10 08:53:55.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.433][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.434][private$selectFields]
biodb.TRACE[2024-06-10 08:53:55.435][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:55.436][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:55.437][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.438][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.438][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.440][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.441][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.442][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.444][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.444][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.454][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.455][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.456][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.458][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.459][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:55.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.470][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 08:53:55.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.492][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.493][private$selectFields]
biodb.TRACE[2024-06-10 08:53:55.493][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:55.494][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:55.495][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.496][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.497][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.498][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.499][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.500][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.502][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.503][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.503][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.505][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.507][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.507][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:55.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.519][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-10 08:53:55.520][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 08:53:55.521][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 08:53:55.531][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 08:53:55.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 08:53:55.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:53:55.539][biodb::testThat]
biodb.INFO [2024-06-10 08:53:55.540][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-10 08:53:55.541][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:55.541][biodb::testThat]
biodb.TRACE[2024-06-10 08:53:55.545][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 08:53:55.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 08:53:55.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:55.578][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:55.582][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:55.583][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-10 08:53:55.584][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:55.586][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-10 08:53:55.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.610][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:55.614][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:55.615][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-10 08:53:55.616][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:55.618][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-10 08:53:55.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:55.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.678][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 08:53:55.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.698][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.699][private$selectFields]
biodb.TRACE[2024-06-10 08:53:55.699][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:55.700][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:55.701][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.702][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.703][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.705][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.706][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.707][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.708][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.709][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.711][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.712][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.713][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.715][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.716][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:55.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.728][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-10 08:53:55.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.738][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.748][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.749][private$selectFields]
biodb.TRACE[2024-06-10 08:53:55.750][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:55.751][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:55.752][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.752][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.754][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.755][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.756][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.757][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.759][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.759][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.760][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.761][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.762][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.764][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.765][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:55.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.779][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 08:53:55.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.788][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.798][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.799][private$selectFields]
biodb.TRACE[2024-06-10 08:53:55.800][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:55.801][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:55.802][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.803][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.804][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.806][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.807][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.808][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.809][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.810][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.811][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.812][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.813][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.814][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.815][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:55.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.826][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-10 08:53:55.827][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 08:53:55.828][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 08:53:55.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:55.868][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:55.872][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:55.874][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-10 08:53:55.875][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:55.876][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-10 08:53:55.880][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:55.883][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:55.885][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-10 08:53:55.886][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:55.887][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-10 08:53:55.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:55.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:55.954][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 08:53:55.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:55.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:55.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:55.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:55.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:55.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:55.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:55.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.974][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.975][private$selectFields]
biodb.TRACE[2024-06-10 08:53:55.975][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:55.976][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:55.977][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.977][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.978][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.980][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.980][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.995][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:55.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:55.997][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:55.998][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:55.999][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.000][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.000][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.002][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.003][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:56.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.017][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-10 08:53:56.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.029][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[2024-06-10 08:53:56.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.036][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.037][private$selectFields]
biodb.TRACE[2024-06-10 08:53:56.038][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:56.039][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:56.039][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.040][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.041][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.043][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.043][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.044][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.046][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.046][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.047][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.048][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.049][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.050][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.051][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:56.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.063][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 08:53:56.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.087][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.089][private$selectFields]
biodb.TRACE[2024-06-10 08:53:56.090][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:56.091][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:56.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.093][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.094][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.096][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.097][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.098][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.100][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.101][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.102][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.103][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.104][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.105][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.106][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:56.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.120][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-10 08:53:56.122][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 08:53:56.123][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 08:53:56.135][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 08:53:56.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 08:53:56.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:53:56.145][biodb::testThat]
biodb.INFO [2024-06-10 08:53:56.146][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-10 08:53:56.147][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:56.148][biodb::testThat]
biodb.TRACE[2024-06-10 08:53:56.152][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 08:53:56.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 08:53:56.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:56.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:56.205][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:56.209][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:56.211][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-10 08:53:56.213][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:56.215][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-10 08:53:56.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:56.243][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:56.246][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:56.248][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-10 08:53:56.249][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:56.251][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-10 08:53:56.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:56.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:56.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:56.299][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 08:53:56.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.320][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.320][private$selectFields]
biodb.TRACE[2024-06-10 08:53:56.321][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:56.322][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:56.323][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.324][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.325][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.326][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.327][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.328][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.330][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.331][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.332][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.333][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.334][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.335][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.336][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:56.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.350][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-10 08:53:56.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.389][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.390][private$selectFields]
biodb.TRACE[2024-06-10 08:53:56.407][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:56.408][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:56.409][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.410][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.411][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.413][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.414][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.415][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.417][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.418][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.419][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.419][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.420][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.422][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.423][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:56.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.437][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 08:53:56.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.456][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.457][private$selectFields]
biodb.TRACE[2024-06-10 08:53:56.457][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:56.458][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:56.459][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.460][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.461][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.462][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.463][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.464][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.466][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.467][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.468][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.468][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.469][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.471][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.472][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:56.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.487][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-10 08:53:56.493][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 08:53:56.494][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 08:53:56.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:56.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:56.618][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:56.626][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:56.627][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-10 08:53:56.629][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:56.635][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-10 08:53:56.642][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:53:56.648][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:53:56.650][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-10 08:53:56.654][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:53:56.656][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-10 08:53:56.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:56.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:56.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:56.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:56.803][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 08:53:56.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.847][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.850][private$selectFields]
biodb.TRACE[2024-06-10 08:53:56.851][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:56.852][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:56.853][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.858][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.860][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.864][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.870][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.872][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.874][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.875][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.877][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.879][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.880][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:56.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.892][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-10 08:53:56.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.902][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.TRACE[2024-06-10 08:53:56.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.910][private$selectFields]
biodb.TRACE[2024-06-10 08:53:56.911][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:56.912][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:56.912][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.913][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.914][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.916][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.916][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.917][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.919][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.919][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.920][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.921][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.922][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.923][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.924][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:56.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.935][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 08:53:56.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:56.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:56.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:56.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:56.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:56.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:56.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:56.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.967][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.968][private$selectFields]
biodb.TRACE[2024-06-10 08:53:56.969][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 08:53:56.970][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 08:53:56.971][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.972][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.973][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.975][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.976][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.977][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.978][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.979][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.980][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 08:53:56.981][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.982][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.983][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.984][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 08:53:56.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:56.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:56.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:56.998][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-10 08:53:56.999][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 08:53:57.000][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 08:53:57.025][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 08:53:57.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 08:53:57.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:57.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 08:53:57.034][biodb::testThat]
biodb.INFO [2024-06-10 08:53:57.035][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-10 08:53:57.036][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:57.036][biodb::testThat]
biodb.DEBUG[2024-06-10 08:53:57.038][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-10 08:53:57.039][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:53:57.041][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-10 08:53:57.042][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:53:57.044][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:57.045][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:57.046][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:57.047][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:57.048][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:57.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:57.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:57.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:57.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:57.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:57.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:57.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:57.076][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-06-10 08:53:57.082][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:57.083][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:57.089][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-06-10 08:53:57.535][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-06-10 08:53:57.928][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:57.932][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-06-10 08:53:57.945][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-06-10 08:53:57.950][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-06-10 08:53:57.952][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:53:57.957][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:53:57.959][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:53:57.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:57.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:57.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:57.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:57.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:57.978][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:57.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:53:57.987][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:57.989][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:57.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:57.995][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:57.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:57.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:58.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.003][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:53:58.007][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:53:58.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.009][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.014][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:53:58.015][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:53:58.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.017][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.022][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:53:58.023][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:53:58.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.025][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.029][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:53:58.030][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:53:58.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.036][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.038][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:58.038][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:53:58.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.044][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.045][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:53:58.051][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:53:58.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.052][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.056][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:58.057][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:53:58.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.064][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.065][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:53:58.066][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:53:58.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.072][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.074][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:53:58.077][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:53:58.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.083][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.085][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:53:58.086][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:53:58.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.092][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:58.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:58.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:58.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:58.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:58.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:58.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:53:58.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:53:58.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:58.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:58.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:58.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:58.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:58.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:58.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:58.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:58.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:58.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:58.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:53:58.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:53:58.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:53:58.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:53:58.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:53:58.154][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-06-10 08:53:58.154][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-10 08:53:58.165][biodb::testThat]
biodb.INFO [2024-06-10 08:53:58.166][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-10 08:53:58.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:53:58.167][biodb::testThat]
biodb.DEBUG[2024-06-10 08:53:58.181][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-06-10 08:53:58.183][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-06-10 08:53:58.184][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-06-10 08:53:58.190][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-06-10 08:53:58.192][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-06-10 08:53:58.197][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:53:58.199][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:53:58.200][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:53:58.203][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:53:58.204][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:53:58.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:58.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:58.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:58.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:58.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:58.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:58.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:58.238][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-06-10 08:53:58.244][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:58.248][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:58.251][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-06-10 08:53:58.625][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-06-10 08:53:59.012][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:59.017][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-06-10 08:53:59.026][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-06-10 08:53:59.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:59.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:59.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:59.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:59.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:59.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:59.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:59.055][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-06-10 08:53:59.060][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:59.061][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:59.064][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-06-10 08:53:59.443][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-06-10 08:53:59.825][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:53:59.830][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-06-10 08:53:59.837][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-06-10 08:53:59.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:53:59.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:53:59.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:53:59.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:53:59.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:53:59.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:53:59.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:53:59.866][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-06-10 08:53:59.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:53:59.875][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:53:59.877][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-06-10 08:54:00.261][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-06-10 08:54:00.652][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:00.659][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-06-10 08:54:00.668][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-06-10 08:54:00.673][private$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[2024-06-10 08:54:00.676][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:54:00.681][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-06-10 08:54:00.683][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-06-10 08:54:00.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:00.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:00.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:00.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:00.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:00.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:00.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:54:00.716][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:00.718][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:00.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.723][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:00.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:00.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.793][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:54:00.797][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:54:00.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.800][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.807][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:00.808][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:00.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.813][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.814][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:54:00.818][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:54:00.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.821][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.825][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:54:00.826][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:54:00.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.832][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.833][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:00.834][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:00.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.838][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.840][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:54:00.845][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:54:00.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.847][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.851][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:00.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:00.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.855][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.860][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:00.861][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:00.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.867][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.869][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:54:00.875][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:54:00.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.877][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.881][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:54:00.883][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:54:00.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.885][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:00.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:00.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:00.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:00.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:00.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:00.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:00.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:00.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:00.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:00.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:00.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:00.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:00.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:00.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:00.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:00.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:00.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:00.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:00.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:00.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:00.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:54:00.968][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:00.969][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:00.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.975][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:00.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:00.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.985][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:54:00.987][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:54:00.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:00.989][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:00.995][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:54:00.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:54:00.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.005][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:01.006][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:01.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.010][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.017][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:01.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:01.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.026][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:54:01.030][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:54:01.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.033][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:54:01.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:54:01.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.047][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:54:01.048][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:54:01.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.054][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:54:01.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:54:01.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.068][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:01.069][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:01.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.076][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.078][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:01.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:01.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.082][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:54:01.083][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:54:01.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.084][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.085][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:54:01.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:54:01.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.089][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:01.090][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:01.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.091][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:01.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:01.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.096][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:01.097][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:01.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.099][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:01.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:01.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.104][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:54:01.105][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:54:01.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.107][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.108][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:54:01.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:54:01.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.112][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:54:01.113][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:54:01.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.114][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.115][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:54:01.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:54:01.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:01.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:01.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:01.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:01.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:01.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:01.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:01.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:54:01.168][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.170][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.172][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.179][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:54:01.180][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:54:01.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.183][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.184][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:54:01.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:54:01.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.190][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:01.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:01.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.194][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:01.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:01.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.200][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:54:01.202][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:54:01.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.204][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:54:01.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:54:01.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.211][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:54:01.212][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:54:01.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.214][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:54:01.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:54:01.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.221][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:01.222][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:01.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.224][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.226][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:01.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:01.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.232][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:54:01.233][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:54:01.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.236][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.238][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:54:01.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:54:01.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.244][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:01.245][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:01.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.248][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:01.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:01.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.254][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:01.256][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:01.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.257][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:01.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:01.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.261][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:54:01.262][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:54:01.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.264][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.265][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:54:01.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:54:01.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.268][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:54:01.269][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:54:01.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.270][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.272][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:54:01.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:54:01.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:01.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:01.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:01.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:01.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:01.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:01.340][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-06-10 08:54:01.340][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-10 08:54:01.341][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-06-10 08:54:01.356][biodb::testThat]
biodb.INFO [2024-06-10 08:54:01.357][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-10 08:54:01.358][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:01.359][biodb::testThat]
biodb.INFO [2024-06-10 08:54:01.384][biodb::testThat]
biodb.INFO [2024-06-10 08:54:01.385][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-10 08:54:01.386][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:01.386][biodb::testThat]
biodb.INFO [2024-06-10 08:54:01.396][biodb::testThat]
biodb.INFO [2024-06-10 08:54:01.397][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-10 08:54:01.398][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:01.399][biodb::testThat]
biodb.DEBUG[2024-06-10 08:54:01.402][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:54:01.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:01.406][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:01.408][private$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[2024-06-10 08:54:01.870][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[2024-06-10 08:54:02.400][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:02.407][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-06-10 08:54:02.418][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-06-10 08:54:02.449][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:02.450][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:02.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:02.452][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:02.456][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:02.457][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:02.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:02.463][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 08:54:02.465][biodb::testThat]
biodb.INFO [2024-06-10 08:54:02.468][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-10 08:54:02.469][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:02.470][biodb::testThat]
biodb.ERROR[2024-06-10 08:54:02.503][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-10 08:54:02.538][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-10 08:54:02.565][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 08:54:02.569][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-10 08:54:02.570][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-10 08:54:02.572][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 08:54:02.575][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:02.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:02.577][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:02.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:02.583][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-10 08:54:02.609][biodb::testContext]
biodb.INFO [2024-06-10 08:54:02.610][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:54:02.611][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-06-10 08:54:02.611][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:54:02.614][biodb::testContext]
biodb.INFO [2024-06-10 08:54:02.617][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:54:02.623][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 08:54:02.631][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:02.632][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 08:54:02.636][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 08:54:02.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.642][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 08:54:02.643][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 08:54:02.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.652][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 08:54:02.653][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 08:54:02.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.659][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 08:54:02.664][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 08:54:02.666][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 08:54:02.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.670][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[2024-06-10 08:54:02.671][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 08:54:02.672][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 08:54:02.676][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 08:54:02.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.683][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 08:54:02.684][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 08:54:02.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.692][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 08:54:02.693][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 08:54:02.694][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 08:54:02.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.698][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 08:54:02.699][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 08:54:02.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.703][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 08:54:02.704][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 08:54:02.705][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 08:54:02.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.709][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:54:02.710][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 08:54:02.711][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 08:54:02.711][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 08:54:02.712][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 08:54:02.714][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 08:54:02.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.718][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.DEBUG[2024-06-10 08:54:02.723][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 08:54:02.725][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 08:54:02.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.729][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 08:54:02.730][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 08:54:02.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.738][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 08:54:02.740][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 08:54:02.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.743][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 08:54:02.749][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 08:54:02.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.753][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 08:54:02.754][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 08:54:02.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.757][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:54:02.758][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 08:54:02.811][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 08:54:02.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.816][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 08:54:02.817][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 08:54:02.818][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 08:54:02.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:02.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:02.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:02.822][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 08:54:02.824][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.825][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-10 08:54:02.827][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.828][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:02.830][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.830][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.831][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.832][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.833][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:54:02.834][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:02.835][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.836][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 08:54:02.837][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:02.838][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.839][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.839][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:02.839][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:02.839][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:02.839][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:54:02.839][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:54:02.840][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:02.842][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:02.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:02.844][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:02.844][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:02.845][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:02.846][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.848][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.849][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:02.850][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:02.851][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.852][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.853][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 08:54:02.855][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.856][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:54:02.857][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.858][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:02.859][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.859][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.860][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.861][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.862][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:54:02.863][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:02.863][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.864][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 08:54:02.865][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:02.866][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.867][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.868][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:02.868][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:02.868][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:02.868][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:54:02.868][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:54:02.889][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:02.891][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:02.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:02.893][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:02.897][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:02.898][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:02.899][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.900][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.901][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:02.903][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:02.904][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.906][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.907][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 08:54:02.909][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.914][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-10 08:54:02.915][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.916][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:02.918][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.919][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.920][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.921][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.922][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:54:02.923][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:02.924][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.925][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 08:54:02.926][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:02.928][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.929][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.930][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.934][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:02.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:02.937][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:02.938][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:02.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:02.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:02.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.947][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.948][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:02.949][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:02.950][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.954][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.955][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 08:54:02.958][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.960][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:54:02.961][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.965][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:02.967][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.970][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.972][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.973][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:02.977][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:54:02.978][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:02.980][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:02.985][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 08:54:02.987][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:02.988][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.991][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:02.993][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:02.995][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:02.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:02.999][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:03.000][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:03.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:03.003][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:03.004][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:03.005][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:03.006][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:03.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:03.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:03.009][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:03.015][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:03.016][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.024][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[2024-06-10 08:54:03.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.028][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[2024-06-10 08:54:03.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.044][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[2024-06-10 08:54:03.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.048][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[2024-06-10 08:54:03.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.052][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[2024-06-10 08:54:03.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.057][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[2024-06-10 08:54:03.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.062][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[2024-06-10 08:54:03.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.066][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[2024-06-10 08:54:03.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.077][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.DEBUG[2024-06-10 08:54:03.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.080][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[2024-06-10 08:54:03.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.084][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 08:54:03.086][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 08:54:03.087][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 08:54:03.088][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 08:54:03.089][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:54:03.090][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 08:54:03.091][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 08:54:03.093][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 08:54:03.094][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 08:54:03.096][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 08:54:03.097][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:54:03.098][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 08:54:03.100][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 08:54:03.101][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 08:54:03.103][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 08:54:03.104][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 08:54:03.106][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 08:54:03.107][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 08:54:03.108][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:54:03.109][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 08:54:03.111][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 08:54:03.112][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 08:54:03.114][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 08:54:03.115][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 08:54:03.117][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 08:54:03.118][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 08:54:03.119][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 08:54:03.120][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 08:54:03.125][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 08:54:03.126][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 08:54:03.128][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 08:54:03.129][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 08:54:03.131][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 08:54:03.132][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 08:54:03.134][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 08:54:03.135][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 08:54:03.136][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 08:54:03.138][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 08:54:03.139][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 08:54:03.141][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 08:54:03.142][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 08:54:03.144][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 08:54:03.145][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 08:54:03.147][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 08:54:03.148][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 08:54:03.149][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 08:54:03.151][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 08:54:03.152][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 08:54:03.154][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 08:54:03.156][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 08:54:03.157][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 08:54:03.159][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 08:54:03.160][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 08:54:03.162][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 08:54:03.164][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 08:54:03.165][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 08:54:03.167][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 08:54:03.169][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 08:54:03.170][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 08:54:03.172][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 08:54:03.173][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 08:54:03.175][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 08:54:03.179][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 08:54:03.181][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 08:54:03.183][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 08:54:03.185][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 08:54:03.191][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:54:03.193][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:54:03.194][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 08:54:03.199][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 08:54:03.201][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 08:54:03.205][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 08:54:03.207][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 08:54:03.213][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 08:54:03.215][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 08:54:03.219][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 08:54:03.221][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 08:54:03.226][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 08:54:03.228][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 08:54:03.234][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 08:54:03.236][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 08:54:03.242][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 08:54:03.246][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 08:54:03.252][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 08:54:03.254][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:54:03.259][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:03.260][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.265][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:03.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:03.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:03.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:03.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:03.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:03.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:03.426][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-10 08:54:03.431][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-10 08:54:03.437][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:03.439][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 08:54:03.444][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:03.445][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:03.446][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:03.451][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:03.453][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:03.454][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-10 08:54:03.458][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-10 08:54:03.459][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:03.461][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:03.466][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-10 08:54:03.468][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-10 08:54:03.469][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-10 08:54:03.470][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:03.471][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:03.471][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:03.471][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:03.472][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-10 08:54:03.473][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:03.474][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:03.475][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:03.476][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:03.477][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:03.478][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:03.479][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:54:03.479][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-10 08:54:03.480][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:03.481][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:03.482][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:03.483][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-10 08:54:03.483][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-10 08:54:03.490][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:54:03.492][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:54:03.494][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-10 08:54:03.496][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:54:03.498][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:54:03.500][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:54:03.504][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-10 08:54:03.505][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-10 08:54:03.507][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-10 08:54:03.509][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-10 08:54:03.510][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 08:54:03.511][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 08:54:03.513][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-10 08:54:03.514][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-10 08:54:03.516][biodb::testThat]
biodb.INFO [2024-06-10 08:54:03.518][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-06-10 08:54:03.519][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:03.520][biodb::testThat]
biodb.DEBUG[2024-06-10 08:54:03.525][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-10 08:54:03.530][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:03.532][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:03.534][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-06-10 08:54:03.903][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-06-10 08:54:04.444][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:04.451][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-06-10 08:54:04.461][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-06-10 08:54:04.472][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:54:04.479][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:04.481][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:04.483][private$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[2024-06-10 08:54:04.862][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[2024-06-10 08:54:05.247][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:05.253][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-06-10 08:54:05.260][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-06-10 08:54:05.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:05.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:05.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:05.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:05.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:05.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:05.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:05.296][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[2024-06-10 08:54:05.302][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:05.307][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:05.309][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-10 08:54:05.701][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-10 08:54:06.105][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:06.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-06-10 08:54:06.120][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-06-10 08:54:06.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:06.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:06.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:06.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:06.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:06.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:06.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:06.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:06.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:06.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:06.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:06.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:06.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:06.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:06.174][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:54:06.179][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:54:06.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-10 08:54:06.182][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:06.184][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-10 08:54:06.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:06.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:06.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:06.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:06.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:06.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:06.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:06.208][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:54:06.212][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:54:06.214][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-10 08:54:06.216][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:06.218][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-10 08:54:06.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:06.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:06.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:06.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:06.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:06.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:06.231][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[2024-06-10 08:54:06.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:06.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:06.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:06.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:06.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:06.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:06.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:06.247][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:54:06.256][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:54:06.261][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-10 08:54:06.262][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:06.268][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-10 08:54:06.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:06.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:06.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:06.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:06.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:06.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:06.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:06.297][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:54:06.304][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:54:06.307][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-10 08:54:06.309][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:06.315][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-10 08:54:06.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:06.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:06.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:06.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:06.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:06.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:06.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:06.345][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:54:06.353][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:06.356][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:06.358][private$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[2024-06-10 08:54:06.743][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[2024-06-10 08:54:07.122][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:07.127][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-06-10 08:54:07.134][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-06-10 08:54:07.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:07.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:07.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:07.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:07.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:07.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:07.213][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.INFO [2024-06-10 08:54:07.226][biodb::testThat]
biodb.INFO [2024-06-10 08:54:07.230][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-06-10 08:54:07.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:07.233][biodb::testThat]
biodb.DEBUG[2024-06-10 08:54:07.239][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[2024-06-10 08:54:07.244][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:07.249][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:07.251][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-10 08:54:07.751][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-10 08:54:08.138][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:08.146][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-06-10 08:54:08.156][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-06-10 08:54:08.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:08.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:08.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:08.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:08.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:08.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:08.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:08.191][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:54:08.196][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:08.197][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:08.203][private$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[2024-06-10 08:54:08.573][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[2024-06-10 08:54:08.948][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:08.951][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-06-10 08:54:08.957][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-06-10 08:54:08.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:08.963][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:08.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:08.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:08.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:08.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:08.974][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.INFO [2024-06-10 08:54:08.982][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 08:54:08.983][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-10 08:54:08.984][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-10 08:54:08.987][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 08:54:08.988][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:08.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:08.990][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:08.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:08.992][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:08.993][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.INFO [2024-06-10 08:54:09.000][biodb::testContext]
biodb.INFO [2024-06-10 08:54:09.003][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:54:09.005][biodb::testContext] Test context - Test web services
biodb.INFO [2024-06-10 08:54:09.006][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:54:09.006][biodb::testContext]
biodb.INFO [2024-06-10 08:54:09.009][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:54:09.013][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 08:54:09.019][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:09.021][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 08:54:09.025][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 08:54:09.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.031][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 08:54:09.032][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 08:54:09.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.035][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 08:54:09.036][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 08:54:09.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.044][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 08:54:09.046][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 08:54:09.047][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 08:54:09.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.053][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 08:54:09.054][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 08:54:09.055][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 08:54:09.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.063][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 08:54:09.064][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 08:54:09.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.071][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 08:54:09.073][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 08:54:09.073][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 08:54:09.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.081][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 08:54:09.083][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 08:54:09.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.086][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[2024-06-10 08:54:09.091][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 08:54:09.092][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 08:54:09.093][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 08:54:09.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.098][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:54:09.101][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 08:54:09.103][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 08:54:09.104][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 08:54:09.108][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 08:54:09.109][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 08:54:09.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.111][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[2024-06-10 08:54:09.114][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 08:54:09.116][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 08:54:09.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.123][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 08:54:09.124][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 08:54:09.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.128][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[2024-06-10 08:54:09.128][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 08:54:09.132][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 08:54:09.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.137][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 08:54:09.139][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 08:54:09.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.145][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 08:54:09.146][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 08:54:09.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.151][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:54:09.155][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 08:54:09.194][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 08:54:09.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.197][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[2024-06-10 08:54:09.200][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 08:54:09.201][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 08:54:09.202][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 08:54:09.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.212][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 08:54:09.215][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.219][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-10 08:54:09.220][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.222][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:09.225][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.226][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.227][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.228][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.232][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:54:09.233][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:09.234][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.237][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 08:54:09.239][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:09.240][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.243][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.244][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:09.244][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:09.244][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:09.244][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:54:09.244][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:54:09.246][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:09.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:09.250][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:09.251][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:09.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:09.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:09.257][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.258][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.259][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:09.262][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:09.264][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.268][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.269][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 08:54:09.273][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.275][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:54:09.276][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.277][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:09.281][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.282][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.283][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.286][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.287][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:54:09.288][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:09.289][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.293][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 08:54:09.294][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:09.295][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.299][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.300][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:09.300][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:09.300][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:09.300][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:54:09.300][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:54:09.301][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:09.302][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:09.304][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:09.306][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:09.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:09.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:09.313][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.314][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.315][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:09.316][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:09.317][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.320][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.321][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 08:54:09.327][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.328][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-10 08:54:09.330][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.332][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:09.334][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.336][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.337][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.341][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.344][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:54:09.345][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:09.347][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.349][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 08:54:09.350][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:09.354][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.355][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.358][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.359][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:09.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:09.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:09.365][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:09.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:09.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:09.372][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.373][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.377][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:09.378][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:09.381][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.383][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.385][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 08:54:09.387][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.388][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:54:09.390][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.391][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:09.392][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.395][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.396][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.397][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.400][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:54:09.402][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:09.403][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.406][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 08:54:09.408][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:09.410][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.411][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.413][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.416][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:09.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:09.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:09.419][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:09.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:09.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:09.422][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.423][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.425][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:09.427][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:09.428][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.429][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:09.431][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:09.433][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.445][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.DEBUG[2024-06-10 08:54:09.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.521][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[2024-06-10 08:54:09.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.558][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[2024-06-10 08:54:09.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.587][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 08:54:09.589][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 08:54:09.593][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 08:54:09.597][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 08:54:09.599][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:54:09.601][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 08:54:09.603][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 08:54:09.605][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 08:54:09.608][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 08:54:09.610][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 08:54:09.612][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:54:09.613][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 08:54:09.615][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 08:54:09.618][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 08:54:09.619][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 08:54:09.623][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 08:54:09.625][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 08:54:09.627][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 08:54:09.629][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:54:09.631][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 08:54:09.635][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 08:54:09.636][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 08:54:09.639][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 08:54:09.641][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 08:54:09.643][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 08:54:09.645][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 08:54:09.646][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 08:54:09.649][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 08:54:09.651][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 08:54:09.653][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 08:54:09.655][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 08:54:09.657][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 08:54:09.660][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 08:54:09.661][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 08:54:09.663][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 08:54:09.664][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 08:54:09.666][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 08:54:09.668][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 08:54:09.669][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 08:54:09.671][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 08:54:09.672][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 08:54:09.673][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 08:54:09.675][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 08:54:09.676][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 08:54:09.677][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 08:54:09.679][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 08:54:09.680][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 08:54:09.681][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 08:54:09.683][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 08:54:09.684][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 08:54:09.685][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 08:54:09.687][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 08:54:09.688][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 08:54:09.690][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 08:54:09.692][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 08:54:09.694][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 08:54:09.695][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 08:54:09.696][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 08:54:09.697][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 08:54:09.699][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 08:54:09.700][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 08:54:09.701][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 08:54:09.702][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 08:54:09.704][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 08:54:09.705][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 08:54:09.706][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 08:54:09.707][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:54:09.708][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:54:09.710][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 08:54:09.711][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 08:54:09.712][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 08:54:09.713][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 08:54:09.714][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 08:54:09.716][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 08:54:09.717][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 08:54:09.718][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 08:54:09.720][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 08:54:09.721][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 08:54:09.723][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 08:54:09.726][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 08:54:09.727][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 08:54:09.731][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 08:54:09.733][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 08:54:09.736][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 08:54:09.738][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:54:09.741][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:09.742][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.743][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.814][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.DEBUG[2024-06-10 08:54:09.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:09.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.837][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[2024-06-10 08:54:09.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:09.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:09.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:09.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:09.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:09.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:09.843][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[2024-06-10 08:54:09.845][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-10 08:54:09.847][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-10 08:54:09.850][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.851][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.852][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.854][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:09.855][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.856][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.857][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.858][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-10 08:54:09.859][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-10 08:54:09.860][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:09.862][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.863][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-10 08:54:09.864][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-10 08:54:09.865][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-10 08:54:09.868][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:09.869][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:09.869][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:09.869][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:09.870][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-10 08:54:09.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:09.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:09.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:09.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:09.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:09.875][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:09.876][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:54:09.876][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-10 08:54:09.877][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:09.878][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:09.879][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:09.880][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-10 08:54:09.880][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-10 08:54:09.881][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:54:09.883][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:54:09.884][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-10 08:54:09.903][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:54:09.905][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:54:09.906][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:54:09.914][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-10 08:54:09.915][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-10 08:54:09.917][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-10 08:54:09.918][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-10 08:54:09.919][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 08:54:09.920][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 08:54:09.921][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-10 08:54:09.922][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-10 08:54:09.923][biodb::testThat]
biodb.INFO [2024-06-10 08:54:09.924][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-06-10 08:54:09.925][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:09.926][biodb::testThat]
biodb.DEBUG[2024-06-10 08:54:09.930][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-10 08:54:09.935][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:54:09.936][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-10 08:54:09.938][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:09.940][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-10 08:54:09.943][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[2024-06-10 08:54:09.947][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:09.950][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:09.952][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-10 08:54:10.324][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-10 08:54:10.700][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:10.704][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-06-10 08:54:10.710][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-06-10 08:54:10.726][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 08:54:10.729][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-10 08:54:10.730][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-10 08:54:10.731][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 08:54:10.732][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:10.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:10.734][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:10.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:10.738][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-10 08:54:10.744][biodb::testContext]
biodb.INFO [2024-06-10 08:54:10.746][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:54:10.746][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-06-10 08:54:10.747][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 08:54:10.748][biodb::testContext]
biodb.INFO [2024-06-10 08:54:10.750][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:54:10.753][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 08:54:10.757][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:10.759][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 08:54:10.760][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 08:54:10.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.768][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 08:54:10.769][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 08:54:10.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.774][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 08:54:10.775][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 08:54:10.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.779][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 08:54:10.781][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 08:54:10.782][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 08:54:10.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.790][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 08:54:10.792][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 08:54:10.794][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 08:54:10.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.800][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 08:54:10.802][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 08:54:10.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.805][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 08:54:10.806][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 08:54:10.807][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 08:54:10.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.812][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 08:54:10.813][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 08:54:10.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.817][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 08:54:10.818][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 08:54:10.819][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 08:54:10.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.822][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[2024-06-10 08:54:10.823][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:54:10.824][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 08:54:10.825][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 08:54:10.826][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 08:54:10.827][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 08:54:10.827][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 08:54:10.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.831][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 08:54:10.832][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 08:54:10.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.837][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 08:54:10.838][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 08:54:10.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.842][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 08:54:10.843][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 08:54:10.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.846][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 08:54:10.847][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 08:54:10.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.850][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 08:54:10.851][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 08:54:10.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.853][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[2024-06-10 08:54:10.853][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 08:54:10.854][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 08:54:10.875][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 08:54:10.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.879][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 08:54:10.880][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 08:54:10.882][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 08:54:10.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:10.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:10.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:10.887][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 08:54:10.890][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:10.893][self$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[2024-06-10 08:54:10.894][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.897][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:10.898][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.899][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:10.900][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:10.901][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:10.902][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:54:10.903][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:10.904][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.905][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 08:54:10.906][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:10.907][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:10.908][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.909][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:10.909][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:10.909][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:10.909][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:54:10.909][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:54:10.910][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:10.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:10.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:10.913][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:10.914][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:10.915][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:10.917][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:10.918][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:10.919][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:10.920][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:10.920][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:10.921][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:10.922][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 08:54:10.925][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:10.927][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:54:10.928][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.929][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:10.930][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.931][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:10.932][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:10.933][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:10.934][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:54:10.935][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:10.935][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.936][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 08:54:10.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:10.939][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:10.941][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.942][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:10.942][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:10.942][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:10.942][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 08:54:10.942][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 08:54:10.943][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:10.944][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:10.945][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:10.946][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:10.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:10.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:10.948][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:10.949][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:10.950][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:10.951][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:10.952][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:10.952][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:10.953][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 08:54:10.955][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.956][self$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[2024-06-10 08:54:10.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:10.959][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.960][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:10.961][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:10.963][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:10.965][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 08:54:10.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:10.968][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:10.969][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 08:54:10.969][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:10.972][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:10.973][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.974][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:10.975][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:10.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:10.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:10.979][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:10.980][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:10.981][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:10.983][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:10.985][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:10.986][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:10.987][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:10.989][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:10.990][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:10.991][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 08:54:10.993][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.995][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 08:54:10.996][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.997][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:10.998][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:10.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:10.999][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:11.000][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 08:54:11.001][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 08:54:11.002][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:11.003][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:11.004][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 08:54:11.005][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:11.006][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:11.007][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:11.009][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:11.010][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 08:54:11.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:11.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:11.012][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:11.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:11.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:11.015][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:11.016][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:11.017][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:11.017][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:11.018][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:11.019][self$setPropertyValue]
biodb.DEBUG[2024-06-10 08:54:11.020][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:11.021][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.053][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[2024-06-10 08:54:11.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.065][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[2024-06-10 08:54:11.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.092][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[2024-06-10 08:54:11.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.102][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[2024-06-10 08:54:11.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.106][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[2024-06-10 08:54:11.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.112][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[2024-06-10 08:54:11.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.118][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[2024-06-10 08:54:11.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.124][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[2024-06-10 08:54:11.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.138][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 08:54:11.140][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 08:54:11.143][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 08:54:11.146][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 08:54:11.148][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:54:11.149][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 08:54:11.150][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 08:54:11.152][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 08:54:11.154][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 08:54:11.156][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 08:54:11.158][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:54:11.159][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 08:54:11.161][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 08:54:11.162][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 08:54:11.163][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 08:54:11.164][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 08:54:11.165][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 08:54:11.167][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 08:54:11.168][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:54:11.169][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 08:54:11.170][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 08:54:11.172][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 08:54:11.174][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 08:54:11.176][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 08:54:11.178][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 08:54:11.180][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 08:54:11.182][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 08:54:11.183][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 08:54:11.185][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 08:54:11.187][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 08:54:11.188][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 08:54:11.191][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 08:54:11.193][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 08:54:11.194][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 08:54:11.196][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 08:54:11.198][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 08:54:11.200][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 08:54:11.202][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 08:54:11.204][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 08:54:11.206][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 08:54:11.207][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 08:54:11.208][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 08:54:11.210][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 08:54:11.211][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 08:54:11.212][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 08:54:11.214][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 08:54:11.215][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 08:54:11.216][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 08:54:11.218][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 08:54:11.220][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 08:54:11.222][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 08:54:11.223][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 08:54:11.225][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 08:54:11.229][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 08:54:11.231][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 08:54:11.233][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 08:54:11.235][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 08:54:11.237][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 08:54:11.238][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 08:54:11.240][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 08:54:11.241][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 08:54:11.242][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 08:54:11.245][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 08:54:11.246][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 08:54:11.249][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 08:54:11.251][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 08:54:11.253][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:54:11.254][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:54:11.256][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 08:54:11.258][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 08:54:11.260][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 08:54:11.262][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 08:54:11.263][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 08:54:11.264][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 08:54:11.265][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 08:54:11.267][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 08:54:11.268][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 08:54:11.269][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 08:54:11.270][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 08:54:11.273][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 08:54:11.274][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 08:54:11.277][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 08:54:11.279][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 08:54:11.282][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 08:54:11.284][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-10 08:54:11.286][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 08:54:11.287][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.290][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.291][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[2024-06-10 08:54:11.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.309][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[2024-06-10 08:54:11.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.338][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[2024-06-10 08:54:11.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.345][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[2024-06-10 08:54:11.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 08:54:11.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.430][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-10 08:54:11.432][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-10 08:54:11.437][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:11.438][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 08:54:11.441][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:11.443][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 08:54:11.444][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:11.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 08:54:11.447][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:11.450][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-10 08:54:11.452][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-10 08:54:11.453][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 08:54:11.454][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:11.455][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-10 08:54:11.458][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-10 08:54:11.459][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-10 08:54:11.462][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 08:54:11.463][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 08:54:11.463][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 08:54:11.463][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 08:54:11.464][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-10 08:54:11.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:11.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:11.469][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 08:54:11.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 08:54:11.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 08:54:11.473][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 08:54:11.474][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:54:11.474][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-10 08:54:11.475][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 08:54:11.476][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 08:54:11.477][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 08:54:11.478][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-10 08:54:11.478][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-10 08:54:11.479][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 08:54:11.481][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 08:54:11.483][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-10 08:54:11.485][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 08:54:11.486][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 08:54:11.488][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 08:54:11.492][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-10 08:54:11.493][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-10 08:54:11.494][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-10 08:54:11.496][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-10 08:54:11.498][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 08:54:11.499][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 08:54:11.518][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-10 08:54:11.519][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-10 08:54:11.521][biodb::testThat]
biodb.INFO [2024-06-10 08:54:11.522][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-06-10 08:54:11.523][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 08:54:11.524][biodb::testThat]
biodb.DEBUG[2024-06-10 08:54:11.528][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-10 08:54:11.532][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:54:11.534][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-10 08:54:11.536][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:11.538][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-10 08:54:11.544][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 08:54:11.548][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 08:54:11.549][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-06-10 08:54:11.551][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 08:54:11.552][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-06-10 08:54:11.558][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-06-10 08:54:11.559][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 08:54:11.560][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-06-10 08:54:11.561][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 08:54:11.562][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 08:54:11.563][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 08:54:11.564][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 08:54:11.565][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 08:54:11.566][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 08:54:11.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:11.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:11.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:11.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:11.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:11.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:11.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 08:54:11.582][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-06-10 08:54:11.585][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 08:54:11.587][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 08:54:11.590][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-06-10 08:54:12.458][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-06-10 08:54:13.504][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 08:54:13.509][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-06-10 08:54:13.517][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-06-10 08:54:13.522][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-06-10 08:54:13.525][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 08:54:13.527][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 08:54:13.530][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 08:54:13.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 08:54:13.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:13.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:13.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:13.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:13.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:13.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 08:54:13.554][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:13.557][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:13.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.558][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:13.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:13.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.570][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:54:13.571][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:54:13.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.573][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.575][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 08:54:13.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 08:54:13.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.581][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:13.582][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:13.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.585][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.588][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 08:54:13.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 08:54:13.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.594][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 08:54:13.596][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 08:54:13.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.600][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.604][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 08:54:13.606][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 08:54:13.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.609][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.611][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:13.616][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:13.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.619][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.622][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:13.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 08:54:13.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.631][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:54:13.632][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:54:13.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.635][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.637][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 08:54:13.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 08:54:13.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.646][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:13.648][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:13.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.649][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:13.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 08:54:13.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.660][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:13.661][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:13.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.665][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 08:54:13.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 08:54:13.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.675][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:54:13.676][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:54:13.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.678][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.682][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 08:54:13.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 08:54:13.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.689][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:54:13.692][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:54:13.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.695][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.697][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 08:54:13.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 08:54:13.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:13.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:13.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:13.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:13.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:13.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:13.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 08:54:13.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 08:54:13.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:13.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:13.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:13.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:13.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:13.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:13.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:13.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:13.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:13.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:13.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 08:54:13.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 08:54:13.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 08:54:13.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 08:54:13.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 08:54:13.766][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-06-10 08:54:13.772][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 08:54:13.776][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-10 08:54:13.777][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-10 08:54:13.778][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 08:54:13.781][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 08:54:13.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 08:54:13.783][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 08:54:13.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 08:54:13.785][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 08:54:13.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 20.934   1.882  65.571

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	2.761	1.306	9.083
ChebiEntry	0.402	0.022	0.654