Multiple platform build/check report for BioC 3.20 - CHECK results for biodbChebi on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4679
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4414
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4441
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4394
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 kjohnson1

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

raw results

Summary

Package: biodbChebi

Version: 1.11.0

Command: /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_1.11.0.tar.gz

StartedAt: 2024-06-10 13:07:26 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 13:08:49 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 83.3 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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 Patched (2024-04-24 r86482) -- "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 13:08:15.910][biodb::testContext]
biodb.INFO [2024-06-10 13:08:15.915][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 13:08:15.916][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-10 13:08:15.917][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 13:08:15.918][biodb::testContext]
biodb.INFO [2024-06-10 13:08:15.927][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-10 13:08:15.930][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 13:08:15.940][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:15.942][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 13:08:15.943][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 13:08:15.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:15.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:15.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:15.946][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 13:08:15.966][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 13:08:15.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:15.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:15.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:15.970][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 13:08:15.971][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 13:08:15.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:15.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:15.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:15.975][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 13:08:15.976][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 13:08:15.977][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 13:08:15.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:15.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:15.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:15.996][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 13:08:15.997][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 13:08:15.998][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 13:08:15.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.002][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 13:08:16.002][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 13:08:16.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.006][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 13:08:16.007][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 13:08:16.008][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 13:08:16.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.011][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 13:08:16.013][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 13:08:16.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.017][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 13:08:16.018][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 13:08:16.019][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 13:08:16.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.022][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 13:08:16.023][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 13:08:16.023][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 13:08:16.024][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 13:08:16.025][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 13:08:16.026][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 13:08:16.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.028][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 13:08:16.029][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 13:08:16.030][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 13:08:16.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.033][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 13:08:16.034][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 13:08:16.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.036][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 13:08:16.037][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 13:08:16.038][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 13:08:16.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.041][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 13:08:16.042][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 13:08:16.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.044][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 13:08:16.045][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 13:08:16.046][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 13:08:16.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.049][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 13:08:16.050][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 13:08:16.062][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 13:08:16.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.065][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 13:08:16.066][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 13:08:16.066][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 13:08:16.067][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 13:08:16.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.074][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 13:08:16.109][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.125][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-10 13:08:16.127][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.128][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:16.129][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.130][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.131][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.132][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.133][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 13:08:16.133][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:16.134][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.135][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 13:08:16.136][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:16.137][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.138][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.138][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:16.138][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:16.138][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:16.138][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 13:08:16.138][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 13:08:16.139][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:16.140][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:16.141][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:16.142][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:16.144][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:16.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:16.145][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.146][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.147][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:16.148][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:16.149][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.149][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.150][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 13:08:16.152][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.153][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 13:08:16.154][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.155][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:16.155][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.156][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.157][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.158][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.158][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 13:08:16.159][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:16.160][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.161][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 13:08:16.162][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:16.162][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.163][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.164][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:16.164][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:16.164][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:16.164][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 13:08:16.164][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 13:08:16.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:16.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:16.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:16.167][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:16.168][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:16.169][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:16.170][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.170][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.171][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:16.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:16.172][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.173][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.174][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 13:08:16.176][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.177][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-10 13:08:16.178][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.178][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:16.179][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.180][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.181][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.182][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.190][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 13:08:16.191][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:16.192][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.193][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 13:08:16.193][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:16.194][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.195][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.196][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.196][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:16.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:16.198][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:16.199][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:16.200][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:16.200][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:16.201][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.202][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.203][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:16.204][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:16.204][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.205][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.206][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 13:08:16.208][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.209][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 13:08:16.210][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.211][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:16.212][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.212][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.213][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.214][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.215][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 13:08:16.216][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:16.216][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.217][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 13:08:16.218][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:16.219][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.220][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.220][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.221][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:16.222][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:16.223][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:16.224][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:16.224][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:16.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:16.226][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.227][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.228][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:16.228][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:16.229][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.230][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:16.235][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:16.236][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.241][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.DEBUG[2024-06-10 13:08:16.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.262][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 13:08:16.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.266][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 13:08:16.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.277][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.DEBUG[2024-06-10 13:08:16.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.293][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 13:08:16.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.295][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 13:08:16.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.301][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 13:08:16.307][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 13:08:16.308][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 13:08:16.310][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 13:08:16.312][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 13:08:16.313][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 13:08:16.314][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 13:08:16.316][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 13:08:16.317][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 13:08:16.318][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 13:08:16.319][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 13:08:16.320][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 13:08:16.321][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 13:08:16.323][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 13:08:16.324][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 13:08:16.325][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 13:08:16.326][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 13:08:16.327][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 13:08:16.328][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 13:08:16.329][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 13:08:16.331][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 13:08:16.332][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 13:08:16.333][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 13:08:16.334][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 13:08:16.335][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 13:08:16.336][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 13:08:16.338][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 13:08:16.339][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 13:08:16.340][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 13:08:16.341][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 13:08:16.342][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 13:08:16.343][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 13:08:16.344][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 13:08:16.346][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 13:08:16.347][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 13:08:16.348][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 13:08:16.349][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 13:08:16.350][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 13:08:16.351][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 13:08:16.352][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 13:08:16.354][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 13:08:16.355][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 13:08:16.357][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 13:08:16.358][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 13:08:16.366][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 13:08:16.368][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 13:08:16.369][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 13:08:16.370][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 13:08:16.372][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 13:08:16.373][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 13:08:16.374][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 13:08:16.375][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 13:08:16.376][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 13:08:16.378][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 13:08:16.379][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 13:08:16.380][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 13:08:16.381][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 13:08:16.382][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 13:08:16.384][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 13:08:16.385][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 13:08:16.386][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 13:08:16.387][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 13:08:16.388][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 13:08:16.389][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 13:08:16.391][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 13:08:16.392][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 13:08:16.393][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 13:08:16.394][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 13:08:16.395][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 13:08:16.397][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 13:08:16.398][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 13:08:16.399][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 13:08:16.400][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 13:08:16.401][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 13:08:16.402][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 13:08:16.404][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 13:08:16.405][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 13:08:16.406][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 13:08:16.407][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 13:08:16.409][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 13:08:16.410][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 13:08:16.411][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 13:08:16.412][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 13:08:16.418][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 13:08:16.420][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-10 13:08:16.424][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:16.425][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.427][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.427][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 13:08:16.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.435][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 13:08:16.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.445][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 13:08:16.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.447][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 13:08:16.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.470][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 13:08:16.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.480][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 13:08:16.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.485][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 13:08:16.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.501][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 13:08:16.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:16.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:16.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:16.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.516][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 13:08:16.518][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-10 13:08:16.535][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-10 13:08:16.537][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.538][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.539][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.540][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:16.541][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.541][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.542][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.543][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-10 13:08:16.544][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-10 13:08:16.545][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:16.546][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.546][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-10 13:08:16.547][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:16.548][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-10 13:08:16.548][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-10 13:08:16.548][self$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 13:08:16.548][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-10 13:08:16.548][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-10 13:08:16.548][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-10 13:08:16.548][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-10 13:08:16.548][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-10 13:08:16.548][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-10 13:08:16.548][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-10 13:08:16.548][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-10 13:08:16.549][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:16.550][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:16.550][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:16.550][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:16.551][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-10 13:08:16.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:16.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:16.553][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:16.554][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:16.555][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:16.555][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:16.556][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:16.556][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-10 13:08:16.557][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:16.558][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:16.558][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:16.559][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-10 13:08:16.559][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-10 13:08:16.565][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 13:08:16.567][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 13:08:16.568][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-10 13:08:16.570][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 13:08:16.571][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 13:08:16.572][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 13:08:16.604][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-10 13:08:16.606][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-10 13:08:16.611][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-10 13:08:16.616][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-10 13:08:16.622][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 13:08:16.623][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 13:08:16.624][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-10 13:08:16.625][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-10 13:08:16.639][biodb::testThat]
biodb.INFO [2024-06-10 13:08:16.640][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-10 13:08:16.641][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:16.641][biodb::testThat]
biodb.TRACE[2024-06-10 13:08:16.646][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 13:08:16.649][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:16.653][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:16.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:16.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:16.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:16.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:16.685][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 13:08:16.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:16.687][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.TRACE[2024-06-10 13:08:16.699][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:16.700][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:16.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.702][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:16.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:16.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.720][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:16.721][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:16.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.722][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.749][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:16.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:16.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.752][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:16.753][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:16.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.755][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:16.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:16.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.772][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:16.774][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:16.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.775][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:16.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:16.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.780][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:16.781][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:16.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.783][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:16.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:16.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.787][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:16.788][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:16.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.790][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.791][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:16.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:16.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.795][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:16.795][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:16.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.797][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.798][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:16.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:16.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.802][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:16.803][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:16.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.804][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:16.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:16.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.809][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:16.810][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:16.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.811][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:16.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:16.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.816][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:16.817][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:16.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.819][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.820][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:16.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:16.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.824][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:16.825][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:16.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.827][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.828][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:16.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:16.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.833][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:16.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:16.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:16.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:16.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:16.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:16.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:16.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:16.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:16.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:16.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:16.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:16.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:16.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:16.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:16.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:16.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:16.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:16.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:16.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:16.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:16.902][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-06-10 13:08:16.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:16.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:16.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:16.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:16.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:16.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:16.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:16.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:16.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:16.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:16.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:16.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:16.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.992][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 13:08:16.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 13:08:16.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.995][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 13:08:16.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 13:08:16.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:16.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:16.998][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 13:08:16.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 13:08:17.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.002][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 13:08:17.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 13:08:17.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.103][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.104][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.106][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.136][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.137][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.138][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.161][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.162][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.163][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.176][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:17.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:17.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:17.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:17.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.183][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:17.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:17.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.187][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:17.187][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:17.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.189][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.190][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:17.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:17.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.213][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.214][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.215][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.238][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.239][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.241][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.254][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:17.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:17.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.258][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:17.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:17.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.262][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:17.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:17.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.272][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:17.274][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:17.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.275][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.276][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:17.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:17.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.288][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.292][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.295][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.299][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.300][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.301][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.302][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.315][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.322][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.326][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.327][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.328][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.329][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.342][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:17.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:17.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.346][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:17.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:17.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.350][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:17.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:17.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.353][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:17.354][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:17.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.356][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.357][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:17.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:17.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.380][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.381][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.383][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:17.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:17.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:17.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:17.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:17.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:17.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.408][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:17.409][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:17.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.411][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:17.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:17.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.424][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.425][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.427][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.438][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:17.439][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:17.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.441][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.446][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:17.447][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:17.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.449][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.453][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:17.455][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:17.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.457][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.462][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.463][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.465][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.470][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.471][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.473][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.478][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.479][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.481][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.485][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.487][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.488][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.493][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.494][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.496][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.501][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.502][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.504][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.510][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:17.511][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:17.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.512][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 13:08:17.521][biodb::testThat]
biodb.INFO [2024-06-10 13:08:17.523][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-10 13:08:17.524][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:17.524][biodb::testThat]
biodb.DEBUG[2024-06-10 13:08:17.540][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-06-10 13:08:17.549][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:17.554][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-06-10 13:08:17.556][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:17.557][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 13:08:17.558][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:17.582][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:17.583][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:17.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:17.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:17.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:17.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:17.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:17.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:17.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:17.597][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.598][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.599][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.628][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:17.629][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:17.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.631][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.632][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:17.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:17.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.635][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:17.636][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:17.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.638][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:17.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:17.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.643][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:17.643][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:17.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.645][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:17.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:17.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.650][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.651][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.652][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:17.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.657][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.657][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.659][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.660][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:17.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.663][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:17.664][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.666][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.667][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:17.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:17.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.670][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.671][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.673][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:17.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.677][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.678][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.679][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.680][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.685][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:17.685][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.687][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.688][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:17.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:17.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.691][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:17.692][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:17.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.694][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:17.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:17.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:17.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:17.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:17.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:17.731][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-06-10 13:08:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-10 13:08:17.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-10 13:08:17.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-10 13:08:17.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-10 13:08:17.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-10 13:08:17.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-10 13:08:17.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 13:08:17.756][biodb::testThat]
biodb.INFO [2024-06-10 13:08:17.757][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-10 13:08:17.758][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:17.758][biodb::testThat]
biodb.TRACE[2024-06-10 13:08:17.761][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.762][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.764][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:17.766][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-06-10 13:08:17.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:17.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:17.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:17.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:17.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:17.806][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-06-10 13:08:17.812][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 13:08:17.833][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:17.849][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-10 13:08:17.851][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:17.852][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 13:08:17.875][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 13:08:17.879][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:17.880][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:17.882][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-10 13:08:18.227][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-10 13:08:18.451][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:18.454][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-10 13:08:18.470][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-10 13:08:18.473][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-06-10 13:08:18.487][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:18.489][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:18.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.490][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.491][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:18.507][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:18.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.512][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 13:08:18.517][biodb::testThat]
biodb.INFO [2024-06-10 13:08:18.519][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-10 13:08:18.519][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:18.520][biodb::testThat]
biodb.TRACE[2024-06-10 13:08:18.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:18.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:18.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:18.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:18.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:18.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:18.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:18.614][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:18.618][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:18.619][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 13:08:18.620][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:18.622][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-06-10 13:08:18.646][biodb::testThat]
biodb.INFO [2024-06-10 13:08:18.647][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-10 13:08:18.648][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:18.649][biodb::testThat]
biodb.TRACE[2024-06-10 13:08:18.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:18.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:18.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:18.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:18.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:18.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:18.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:18.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:18.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:18.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:18.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:18.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:18.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.692][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 13:08:18.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 13:08:18.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.696][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 13:08:18.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 13:08:18.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.699][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 13:08:18.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 13:08:18.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.702][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 13:08:18.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 13:08:18.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:18.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:18.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:18.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:18.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:18.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:18.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:18.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:18.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:18.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:18.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:18.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:18.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.751][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 13:08:18.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 13:08:18.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.755][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-10 13:08:18.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-10 13:08:18.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.758][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-10 13:08:18.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-10 13:08:18.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:18.761][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-10 13:08:18.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-10 13:08:18.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:18.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 13:08:18.772][biodb::testThat]
biodb.INFO [2024-06-10 13:08:18.773][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-10 13:08:18.774][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:18.775][biodb::testThat]
biodb.INFO [2024-06-10 13:08:18.784][biodb::testThat]
biodb.INFO [2024-06-10 13:08:18.785][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-10 13:08:18.786][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:18.786][biodb::testThat]
biodb.INFO [2024-06-10 13:08:18.795][biodb::testThat]
biodb.INFO [2024-06-10 13:08:18.796][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-10 13:08:18.797][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:18.798][biodb::testThat]
biodb.DEBUG[2024-06-10 13:08:18.802][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-06-10 13:08:19.048][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-06-10 13:08:19.358][biodb::testThat]
biodb.INFO [2024-06-10 13:08:19.359][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-10 13:08:19.360][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:19.362][biodb::testThat]
biodb.DEBUG[2024-06-10 13:08:19.472][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 13:08:19.584][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:19.585][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:19.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.587][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:19.588][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:19.589][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:19.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.591][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 13:08:19.593][biodb::testThat]
biodb.INFO [2024-06-10 13:08:19.594][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-10 13:08:19.594][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:19.595][biodb::testThat]
biodb.TRACE[2024-06-10 13:08:19.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:19.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:19.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:19.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:19.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:19.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:19.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:19.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:19.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:19.718][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:19.722][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:19.724][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 13:08:19.725][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:19.726][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-10 13:08:19.798][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:19.801][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:19.802][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 13:08:19.804][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:19.805][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-06-10 13:08:19.820][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 13:08:19.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 13:08:19.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:19.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:19.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:19.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:19.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:19.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:19.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:19.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:19.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:19.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:19.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:19.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:19.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:19.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:19.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:19.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:19.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:19.855][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:19.877][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:19.878][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:19.901][private$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 13:08:19.977][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 13:08:20.052][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:20.054][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-10 13:08:20.059][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-10 13:08:20.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:20.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:20.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:20.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:20.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:20.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:20.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:20.073][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-06-10 13:08:20.122][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:20.125][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-06-10 13:08:20.126][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:20.127][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:20.129][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:20.130][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:20.131][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:20.132][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:20.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:20.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:20.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:20.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:20.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:20.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:20.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:20.148][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-06-10 13:08:20.151][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:20.152][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:20.162][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-06-10 13:08:20.236][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 13:08:20.309][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:20.311][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-06-10 13:08:20.315][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-06-10 13:08:20.318][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-06-10 13:08:20.319][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:20.321][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:20.322][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:20.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:20.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:20.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:20.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:20.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:20.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:20.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:20.335][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:20.337][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:20.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.338][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:20.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:20.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.343][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:20.344][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:20.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.346][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.347][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:20.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:20.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.351][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:20.352][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:20.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.353][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.355][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:20.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:20.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.359][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:20.360][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:20.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.361][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:20.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:20.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.366][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:20.367][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:20.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.368][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:20.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:20.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.373][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:20.374][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:20.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.375][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.377][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:20.378][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.379][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.380][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:20.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.384][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:20.385][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:20.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.386][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:20.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:20.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.391][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:20.392][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:20.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.393][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:20.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:20.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.398][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:20.399][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:20.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.401][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.402][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:20.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:20.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.405][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:20.406][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:20.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.408][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.418][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:20.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:20.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:20.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:20.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:20.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:20.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:20.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:20.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:20.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:20.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:20.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:20.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:20.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:20.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:20.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:20.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:20.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:20.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:20.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:20.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:20.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:20.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:20.457][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-06-10 13:08:20.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:20.478][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 13:08:20.482][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:20.483][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:20.485][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-10 13:08:20.560][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-10 13:08:20.630][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:20.632][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-10 13:08:20.637][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-10 13:08:20.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:20.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:20.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:20.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:20.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:20.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:20.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:20.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:20.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:20.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:20.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:20.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:20.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:20.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:20.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:20.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:20.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:20.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:20.697][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-06-10 13:08:20.698][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:20.699][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-06-10 13:08:20.701][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:20.702][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:20.703][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:20.703][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:20.704][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:20.705][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:20.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:20.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:20.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:20.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:20.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:20.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:20.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:20.730][scheduler$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 13:08:20.733][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:20.734][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-10 13:08:20.735][rule$waitAsNeeded] Wait 0.164903 second(s).
biodb.TRACE[2024-06-10 13:08:21.052][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-06-10 13:08:21.122][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 13:08:21.196][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:21.198][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-06-10 13:08:21.202][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-06-10 13:08:21.204][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-06-10 13:08:21.206][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:21.207][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:21.208][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:21.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:21.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:21.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:21.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:21.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:21.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:21.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:21.221][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.223][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.224][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.229][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:21.230][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:21.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.231][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.232][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:21.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:21.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.246][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:21.247][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:21.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.248][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.250][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:21.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:21.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.253][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:21.254][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:21.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.256][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:21.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:21.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.260][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:21.261][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:21.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.263][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.264][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:21.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:21.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.267][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:21.268][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:21.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.270][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.271][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:21.272][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.273][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.274][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:21.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.278][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:21.278][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:21.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.280][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:21.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:21.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.285][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:21.286][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:21.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.287][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:21.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:21.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.292][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:21.293][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:21.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.295][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.296][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:21.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:21.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.299][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:21.300][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:21.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.301][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.302][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:21.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:21.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:21.345][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-06-10 13:08:21.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:21.375][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 13:08:21.379][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:21.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 13:08:21.381][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:21.383][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 13:08:21.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:21.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:21.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:21.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:21.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:21.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:21.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:21.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:21.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:21.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:21.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:21.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:21.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:21.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:21.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:21.419][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-06-10 13:08:21.420][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:21.421][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-06-10 13:08:21.422][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:21.423][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:21.424][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:21.425][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:21.426][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:21.427][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:21.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:21.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:21.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:21.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:21.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:21.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:21.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:21.441][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-06-10 13:08:21.444][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:21.445][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:21.447][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-06-10 13:08:21.516][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 13:08:21.591][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:21.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-06-10 13:08:21.607][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-06-10 13:08:21.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-06-10 13:08:21.611][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:21.612][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:21.614][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:21.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:21.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:21.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:21.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:21.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:21.626][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:21.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:21.629][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.631][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.632][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.637][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:21.638][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:21.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.640][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.641][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:21.642][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:21.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.644][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.646][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:21.647][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:21.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.649][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.650][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:21.651][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:21.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.653][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.654][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:21.655][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:21.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.656][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.657][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:21.658][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.660][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.661][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:21.662][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:21.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.663][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.664][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:21.665][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:21.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.667][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:21.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:21.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.671][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:21.672][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:21.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.674][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.675][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:21.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:21.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.678][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:21.679][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:21.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.681][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:21.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:21.722][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-06-10 13:08:21.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:21.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:21.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:21.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:21.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:21.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:21.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:21.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:21.753][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 13:08:21.754][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-06-10 13:08:21.755][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:21.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-06-10 13:08:21.757][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:21.758][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:21.759][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:21.760][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:21.761][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:21.762][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:21.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:21.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:21.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:21.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:21.774][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 13:08:21.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:21.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:21.776][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-06-10 13:08:21.779][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:21.780][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:21.782][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-06-10 13:08:21.857][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 13:08:21.938][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:21.941][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-06-10 13:08:21.945][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-06-10 13:08:21.947][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-06-10 13:08:21.949][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:21.950][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:21.951][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:21.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:21.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:21.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:21.960][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:21.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:21.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:21.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:21.966][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.967][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.969][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:21.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:21.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.974][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:21.975][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:21.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.977][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.978][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:21.979][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:21.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.988][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.994][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:21.995][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:21.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:21.997][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:21.999][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:22.000][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:22.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.002][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.003][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:22.005][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:22.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.006][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.007][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:22.008][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.010][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.011][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:22.012][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:22.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.014][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.015][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:22.016][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:22.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.017][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:22.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:22.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.022][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:22.023][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:22.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.025][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.026][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:22.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:22.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.029][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:22.030][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:22.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.032][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:22.068][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-06-10 13:08:22.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:22.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:22.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:22.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:22.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:22.136][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 13:08:22.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:22.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:22.138][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-06-10 13:08:22.139][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:22.141][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-06-10 13:08:22.142][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:22.143][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:22.144][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:22.145][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:22.146][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:22.147][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:22.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:22.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:22.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:22.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:22.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:22.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:22.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:22.161][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-06-10 13:08:22.164][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:22.164][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:22.166][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-06-10 13:08:22.247][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 13:08:22.317][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:22.320][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-06-10 13:08:22.324][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-06-10 13:08:22.327][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-06-10 13:08:22.328][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:22.329][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:22.330][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:22.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:22.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:22.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:22.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:22.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:22.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:22.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:22.344][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.345][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.347][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.352][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:22.353][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:22.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.354][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.355][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:22.356][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:22.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.358][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.359][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:22.360][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:22.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.361][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.362][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:22.363][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:22.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.365][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.366][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:22.367][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:22.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.368][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.369][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:22.370][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.371][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.372][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:22.373][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:22.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.375][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.376][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:22.377][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:22.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:22.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:22.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.384][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:22.385][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:22.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.387][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.388][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:22.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:22.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.403][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:22.404][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:22.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.406][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:22.442][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-06-10 13:08:22.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:22.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:22.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:22.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:22.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:22.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:22.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:22.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:22.471][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-06-10 13:08:22.472][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:22.473][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-06-10 13:08:22.474][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:22.475][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:22.476][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:22.477][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:22.478][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:22.479][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:22.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:22.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:22.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:22.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:22.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:22.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:22.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:22.492][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-06-10 13:08:22.495][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:22.496][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:22.497][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-06-10 13:08:22.573][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 13:08:22.644][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:22.653][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-06-10 13:08:22.662][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-06-10 13:08:22.665][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-06-10 13:08:22.667][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:22.668][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:22.670][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:22.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:22.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:22.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:22.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:22.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:22.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:22.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:22.684][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.685][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.687][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.692][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:22.693][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:22.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.695][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.696][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:22.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:22.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.700][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:22.701][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:22.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.702][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:22.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:22.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.708][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:22.709][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:22.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.711][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.712][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:22.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:22.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.715][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:22.716][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:22.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.718][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:22.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:22.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.722][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:22.723][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:22.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.725][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.726][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:22.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:22.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.729][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:22.730][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.732][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.733][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:22.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.737][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:22.737][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:22.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.739][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:22.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:22.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.744][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:22.745][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:22.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.747][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.748][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:22.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:22.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.752][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:22.753][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:22.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.754][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.755][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:22.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:22.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.759][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:22.760][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:22.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.761][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.762][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:22.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:22.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:22.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:22.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:22.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:22.807][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-06-10 13:08:22.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:22.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:22.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:22.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:22.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:22.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:22.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:22.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:22.826][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 13:08:22.827][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:22.828][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 13:08:22.829][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-06-10 13:08:22.831][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:22.832][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-06-10 13:08:22.834][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:22.835][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:22.836][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:22.837][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:22.838][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:22.838][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:22.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:22.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:22.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:22.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:22.850][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 13:08:22.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:22.852][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 13:08:22.853][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-06-10 13:08:22.856][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:22.857][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:22.859][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-06-10 13:08:22.935][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 13:08:23.013][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:23.016][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-06-10 13:08:23.019][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-06-10 13:08:23.022][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-06-10 13:08:23.024][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:23.025][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:23.026][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:23.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:23.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:23.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:23.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:23.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:23.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:23.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:23.052][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.053][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.055][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.060][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:23.060][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:23.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.062][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.063][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:23.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:23.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.067][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:23.068][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:23.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.069][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:23.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:23.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.074][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:23.075][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:23.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.077][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:23.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:23.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.081][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.082][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.083][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.088][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:23.089][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:23.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.090][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.091][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:23.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:23.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.095][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:23.096][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.097][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.098][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:23.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.101][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.102][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.104][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.108][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:23.109][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:23.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.111][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:23.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:23.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.115][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:23.116][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:23.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.118][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.119][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:23.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:23.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.122][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:23.123][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:23.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.124][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.125][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:23.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:23.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:23.169][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-06-10 13:08:23.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:23.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:23.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:23.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:23.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:23.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:23.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:23.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:23.190][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-06-10 13:08:23.191][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:23.192][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-06-10 13:08:23.193][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:23.194][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:23.195][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:23.196][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:23.197][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:23.198][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:23.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:23.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:23.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:23.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:23.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:23.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:23.209][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 13:08:23.210][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-06-10 13:08:23.213][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:23.214][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:23.215][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-06-10 13:08:23.287][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 13:08:23.363][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:23.366][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-06-10 13:08:23.370][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-06-10 13:08:23.373][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-06-10 13:08:23.374][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:23.375][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:23.376][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:23.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:23.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:23.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:23.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:23.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:23.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:23.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:23.390][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.391][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.393][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.408][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:23.409][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:23.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.411][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.412][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:23.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:23.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.416][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:23.417][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:23.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.418][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.420][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:23.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:23.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.423][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:23.424][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:23.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.426][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:23.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:23.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.430][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.431][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.433][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.434][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.438][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:23.438][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:23.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.440][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.441][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:23.442][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.444][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.445][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:23.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.448][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.449][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.450][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.455][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:23.456][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:23.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.457][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:23.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:23.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.462][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:23.463][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:23.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.464][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.465][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:23.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:23.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.469][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:23.470][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:23.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.471][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.472][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:23.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:23.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:23.517][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-06-10 13:08:23.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:23.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:23.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:23.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:23.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:23.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:23.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:23.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:23.539][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-06-10 13:08:23.540][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:23.541][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-06-10 13:08:23.543][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:23.544][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:23.545][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:23.545][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:23.546][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:23.547][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:23.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:23.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:23.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:23.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:23.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:23.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:23.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:23.561][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-06-10 13:08:23.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:23.565][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:23.566][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-06-10 13:08:23.640][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 13:08:23.711][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:23.714][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-06-10 13:08:23.718][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-06-10 13:08:23.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-06-10 13:08:23.722][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:23.723][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:23.724][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:23.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:23.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:23.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:23.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:23.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:23.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:23.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:23.737][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.738][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.739][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.744][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:23.745][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:23.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.746][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.747][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:23.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:23.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.751][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:23.752][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:23.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.753][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:23.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:23.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.770][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:23.771][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:23.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.773][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:23.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:23.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.778][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.778][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.780][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:23.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.785][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:23.786][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:23.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.787][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.788][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:23.789][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.791][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.792][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:23.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.796][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.796][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.798][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:23.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.802][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:23.803][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:23.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.805][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:23.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:23.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.810][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:23.811][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:23.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.813][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.814][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:23.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:23.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.817][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:23.818][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:23.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.820][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.821][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:23.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:23.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:23.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:23.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:23.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:23.857][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-06-10 13:08:23.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:23.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:23.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:23.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:23.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:23.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:23.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:23.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:23.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:23.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:23.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:23.887][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-06-10 13:08:23.887][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:23.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-06-10 13:08:23.890][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:23.891][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:23.892][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:23.893][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:23.894][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:23.895][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:23.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:23.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:23.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:23.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:23.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:23.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:23.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:23.909][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-06-10 13:08:23.912][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:23.913][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:23.914][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-06-10 13:08:23.985][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 13:08:24.065][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:24.068][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-06-10 13:08:24.072][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-06-10 13:08:24.075][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-06-10 13:08:24.077][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:24.078][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:24.080][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:24.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:24.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:24.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:24.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:24.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:24.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:24.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:24.094][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.095][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.096][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.101][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:24.102][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:24.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.104][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.105][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:24.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:24.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.108][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:24.109][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:24.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.111][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:24.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:24.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.115][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:24.116][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:24.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.118][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:24.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:24.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.124][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.125][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.127][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.143][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:24.144][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:24.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.147][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.148][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:24.149][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.151][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.152][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:24.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.155][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.156][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.158][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.163][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:24.164][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:24.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.165][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:24.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:24.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.170][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:24.171][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:24.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.172][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.173][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:24.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:24.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.176][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:24.177][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:24.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.179][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.180][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:24.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:24.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:24.215][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-06-10 13:08:24.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:24.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:24.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:24.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:24.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:24.240][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 13:08:24.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:24.242][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 13:08:24.244][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-06-10 13:08:24.245][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:24.246][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-06-10 13:08:24.247][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:24.248][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:24.249][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:24.250][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:24.251][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:24.252][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:24.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:24.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:24.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:24.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:24.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:24.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:24.264][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.DEBUG[2024-06-10 13:08:24.265][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-06-10 13:08:24.268][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:24.269][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:24.270][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-06-10 13:08:24.351][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 13:08:24.426][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:24.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-06-10 13:08:24.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-06-10 13:08:24.435][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-06-10 13:08:24.436][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:24.437][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:24.438][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:24.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:24.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:24.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:24.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:24.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:24.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:24.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:24.452][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.453][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.455][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.459][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:24.460][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:24.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.462][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.463][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:24.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:24.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.466][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:24.467][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:24.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.468][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:24.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:24.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.473][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:24.474][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:24.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.476][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:24.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:24.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.481][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.482][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.484][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.489][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:24.490][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:24.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.491][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.493][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:24.493][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.495][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.496][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:24.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.510][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.511][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.513][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.518][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:24.519][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:24.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.521][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:24.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:24.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.525][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:24.526][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:24.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.528][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.529][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:24.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:24.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.532][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:24.533][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:24.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.535][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.536][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:24.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:24.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:24.571][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-06-10 13:08:24.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:24.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:24.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:24.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:24.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:24.589][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 13:08:24.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:24.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:24.592][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-06-10 13:08:24.593][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:24.594][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-06-10 13:08:24.596][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:24.597][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:24.597][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:24.598][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:24.599][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:24.600][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:24.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:24.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:24.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:24.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:24.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:24.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:24.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:24.622][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-06-10 13:08:24.625][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:24.626][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:24.628][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-06-10 13:08:24.699][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 13:08:24.772][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:24.775][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-06-10 13:08:24.779][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-06-10 13:08:24.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-06-10 13:08:24.783][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:24.784][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:24.785][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:24.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:24.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:24.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:24.794][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:24.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:24.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:24.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:24.800][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.802][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.803][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.808][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:24.809][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:24.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.811][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.812][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:24.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:24.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.815][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:24.817][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:24.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.819][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.820][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:24.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:24.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.823][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:24.824][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:24.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.826][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:24.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:24.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.830][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.831][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.833][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:24.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.838][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:24.839][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:24.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.840][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.841][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:24.842][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.844][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.845][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:24.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.848][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.849][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.850][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:24.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.856][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:24.857][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:24.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.859][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:24.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:24.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.876][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:24.877][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:24.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.879][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.881][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:24.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:24.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.884][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:24.885][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:24.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.887][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.888][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:24.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:24.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:24.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:24.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:24.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:24.926][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-06-10 13:08:24.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:24.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:24.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:24.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:24.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:24.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:24.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:24.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:24.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:24.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:24.946][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 13:08:24.947][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-06-10 13:08:24.948][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:24.950][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-06-10 13:08:24.951][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:24.952][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:24.953][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:24.954][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:24.955][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:24.956][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:24.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:24.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:24.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:24.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:24.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:24.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:24.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:24.970][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-06-10 13:08:24.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:24.974][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:24.982][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-06-10 13:08:25.057][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 13:08:25.130][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:25.133][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-06-10 13:08:25.137][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-06-10 13:08:25.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-06-10 13:08:25.141][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:25.142][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:25.143][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:25.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:25.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:25.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:25.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:25.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:25.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:25.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:25.156][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.157][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.159][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.164][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:25.165][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:25.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.166][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.167][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:25.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:25.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.171][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:25.171][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:25.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.173][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.174][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:25.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:25.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.177][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:25.178][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:25.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.180][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.181][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:25.182][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:25.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.185][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.186][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:25.187][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:25.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.189][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.190][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:25.191][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.192][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.194][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:25.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.197][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.198][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.200][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.204][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:25.205][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:25.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.207][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.208][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:25.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:25.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.212][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:25.213][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:25.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.215][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.216][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:25.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:25.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.219][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:25.220][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:25.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.222][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:25.270][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-06-10 13:08:25.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:25.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:25.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:25.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:25.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:25.289][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 13:08:25.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:25.291][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 13:08:25.292][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-06-10 13:08:25.293][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:25.294][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-06-10 13:08:25.296][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:25.297][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:25.298][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:25.298][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:25.299][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:25.300][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:25.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:25.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:25.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:25.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:25.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:25.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:25.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:25.314][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-06-10 13:08:25.317][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:25.318][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:25.319][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-06-10 13:08:25.390][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 13:08:25.463][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:25.466][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-06-10 13:08:25.470][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-06-10 13:08:25.473][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-06-10 13:08:25.475][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:25.477][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:25.478][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:25.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:25.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:25.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:25.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:25.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:25.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:25.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:25.503][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.505][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.507][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.512][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:25.513][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:25.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.515][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.516][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:25.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:25.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.519][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:25.520][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:25.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.522][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:25.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:25.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.527][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:25.528][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:25.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.529][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.530][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:25.531][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:25.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.533][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.534][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:25.535][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:25.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.536][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.538][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:25.538][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.540][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.541][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:25.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.545][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.546][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.547][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.552][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:25.553][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:25.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.554][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:25.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:25.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.559][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:25.561][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:25.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.562][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.563][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:25.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:25.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.567][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:25.568][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:25.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.569][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:25.613][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-06-10 13:08:25.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:25.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:25.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:25.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:25.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:25.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:25.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:25.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:25.635][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-06-10 13:08:25.636][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:25.637][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-06-10 13:08:25.639][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:25.640][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:25.641][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:25.641][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:25.642][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:25.643][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:25.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:25.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:25.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:25.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:25.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:25.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:25.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:25.657][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-06-10 13:08:25.660][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:25.661][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:25.662][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-06-10 13:08:25.737][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 13:08:25.809][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:25.812][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-06-10 13:08:25.815][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-06-10 13:08:25.818][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-06-10 13:08:25.820][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:25.821][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:25.822][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:25.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:25.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:25.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:25.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:25.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:25.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:25.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:25.836][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.837][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.839][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.844][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:25.844][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:25.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.846][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:25.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:25.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.851][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:25.852][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:25.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.853][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.854][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:25.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:25.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.869][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:25.871][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:25.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.873][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:25.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:25.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.878][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:25.878][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:25.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.880][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:25.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:25.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.885][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:25.886][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:25.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.887][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.889][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:25.890][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.893][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:25.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.896][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.897][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.899][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:25.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.904][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:25.904][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:25.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.906][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:25.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:25.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.911][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:25.912][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:25.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.913][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.914][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:25.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:25.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.918][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:25.920][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:25.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.922][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.924][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:25.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:25.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:25.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:25.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:25.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:25.960][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-06-10 13:08:25.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:25.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:25.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:25.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:25.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:25.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:25.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:25.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:25.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:25.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:25.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:25.990][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-06-10 13:08:25.991][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:25.993][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-06-10 13:08:25.994][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:25.995][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:25.996][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:25.997][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:25.998][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:25.998][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:26.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:26.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:26.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:26.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:26.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:26.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:26.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:26.012][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-06-10 13:08:26.016][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:26.017][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:26.018][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-06-10 13:08:26.089][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 13:08:26.162][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:26.165][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-06-10 13:08:26.169][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-06-10 13:08:26.172][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-06-10 13:08:26.174][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:26.176][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:26.177][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:26.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:26.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:26.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:26.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:26.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:26.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:26.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:26.192][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.193][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.194][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.200][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:26.201][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:26.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.203][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.204][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:26.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:26.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.208][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:26.209][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:26.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.210][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.211][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:26.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:26.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.215][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:26.216][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:26.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.218][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:26.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:26.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.222][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.223][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.236][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.247][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:26.248][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:26.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.250][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.252][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:26.253][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.255][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.256][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:26.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.260][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.261][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.262][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.267][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:26.268][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:26.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.270][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:26.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:26.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.275][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:26.276][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:26.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.277][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.278][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:26.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:26.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.282][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:26.283][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:26.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.284][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.285][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:26.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:26.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:26.322][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-06-10 13:08:26.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:26.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:26.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:26.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:26.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:26.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:26.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:26.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:26.352][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-06-10 13:08:26.353][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:26.355][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.INFO [2024-06-10 13:08:26.357][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-10 13:08:26.358][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:26.359][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:26.360][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:26.361][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:26.362][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:26.363][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:26.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:26.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:26.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:26.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:26.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:26.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:26.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:26.376][scheduler$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 13:08:26.379][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:26.380][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:26.382][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-06-10 13:08:26.454][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-06-10 13:08:26.525][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:26.528][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-06-10 13:08:26.532][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-06-10 13:08:26.535][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-06-10 13:08:26.537][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:26.538][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:26.539][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:26.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:26.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:26.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:26.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:26.550][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 13:08:26.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:26.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:26.555][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.556][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.558][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.563][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:26.564][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:26.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.565][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.567][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:26.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:26.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.570][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:26.571][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:26.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.573][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.574][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:26.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:26.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.578][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:26.579][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:26.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.581][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.582][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:26.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:26.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.585][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.586][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.588][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.593][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:26.594][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:26.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.596][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.597][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:26.598][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.600][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.601][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:26.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.616][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.618][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.620][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.625][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:26.625][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:26.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.627][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:26.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:26.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.632][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:26.633][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:26.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.634][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.635][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:26.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:26.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.639][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:26.640][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:26.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.641][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.642][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:26.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:26.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:26.678][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-06-10 13:08:26.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:26.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:26.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:26.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:26.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:26.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:26.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:26.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:26.699][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-06-10 13:08:26.700][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:26.702][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-06-10 13:08:26.703][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:26.704][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:26.705][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:26.706][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:26.707][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:26.707][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:26.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:26.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:26.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:26.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:26.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:26.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:26.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:26.729][scheduler$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 13:08:26.732][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:26.733][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:26.734][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-06-10 13:08:26.809][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-06-10 13:08:26.879][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:26.881][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-06-10 13:08:26.885][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-06-10 13:08:26.888][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-06-10 13:08:26.890][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:26.891][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:26.892][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:26.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:26.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:26.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:26.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:26.901][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 13:08:26.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:26.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:26.905][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.906][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.908][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.913][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:26.914][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:26.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.915][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.916][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:26.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:26.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.920][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:26.921][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:26.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.922][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.923][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:26.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:26.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.927][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:26.927][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:26.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.929][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:26.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:26.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.934][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.934][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.936][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:26.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.940][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:26.941][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:26.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.943][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.944][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:26.945][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.946][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.947][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:26.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:26.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.950][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.951][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.953][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:26.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.957][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:26.958][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:26.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.960][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:26.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:26.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.976][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:26.977][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:26.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.979][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.980][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:26.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:26.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.983][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:26.984][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:26.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.985][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.986][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:26.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:26.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:26.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:26.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:26.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:26.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:26.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:27.022][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-06-10 13:08:27.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:27.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:27.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:27.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:27.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:27.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:27.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:27.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:27.043][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-06-10 13:08:27.044][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:27.045][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-06-10 13:08:27.047][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:27.048][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:27.050][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:27.050][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:27.051][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:27.052][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:27.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:27.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:27.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:27.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:27.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:27.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:27.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:27.066][scheduler$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 13:08:27.075][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:27.077][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:27.079][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-06-10 13:08:27.151][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-06-10 13:08:27.228][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:27.230][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-06-10 13:08:27.234][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-06-10 13:08:27.237][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-06-10 13:08:27.238][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:27.239][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:27.241][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:27.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:27.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:27.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:27.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:27.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:27.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:27.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:27.254][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.255][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.257][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.261][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:27.262][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:27.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.264][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.265][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:27.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:27.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.268][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:27.269][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:27.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.271][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:27.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:27.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.276][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:27.277][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:27.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.278][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:27.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:27.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.283][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.284][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.285][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.286][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.290][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:27.291][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:27.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.292][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.293][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:27.294][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.296][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.297][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:27.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.301][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.302][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.303][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.308][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:27.308][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:27.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.310][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:27.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:27.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.314][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:27.315][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:27.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.317][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.318][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:27.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:27.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.321][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:27.332][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:27.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.335][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.336][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:27.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:27.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:27.374][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-06-10 13:08:27.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:27.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:27.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:27.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:27.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:27.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:27.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:27.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:27.396][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-06-10 13:08:27.397][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:27.398][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-06-10 13:08:27.400][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:27.401][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:27.403][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:27.404][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:27.405][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:27.406][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:27.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:27.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:27.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:27.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:27.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:27.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:27.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:27.420][scheduler$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 13:08:27.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:27.425][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:27.426][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-06-10 13:08:27.507][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-06-10 13:08:27.579][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:27.581][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-06-10 13:08:27.585][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-06-10 13:08:27.588][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-06-10 13:08:27.601][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:27.603][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:27.605][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:27.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:27.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:27.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:27.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:27.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:27.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:27.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:27.621][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.622][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.623][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.628][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:27.629][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:27.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.630][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.632][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:27.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:27.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.635][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:27.636][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:27.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.638][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:27.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:27.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.643][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:27.644][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:27.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.645][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:27.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:27.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.650][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.651][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.652][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.657][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:27.657][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:27.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.659][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.660][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:27.661][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.662][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.663][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:27.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.667][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.668][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.669][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.674][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:27.675][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:27.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.677][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:27.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:27.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.684][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:27.685][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:27.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.686][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.687][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:27.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:27.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.691][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:27.692][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:27.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.693][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.694][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:27.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:27.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:27.744][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-06-10 13:08:27.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:27.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:27.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:27.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:27.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:27.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:27.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:27.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:27.766][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-06-10 13:08:27.767][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:27.771][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-06-10 13:08:27.773][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:27.775][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:27.775][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:27.776][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:27.777][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:27.777][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:27.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:27.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:27.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:27.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:27.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:27.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:27.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:27.785][scheduler$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 13:08:27.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:27.787][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:27.788][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-06-10 13:08:27.857][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-06-10 13:08:27.922][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:27.925][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-06-10 13:08:27.929][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-06-10 13:08:27.931][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-06-10 13:08:27.933][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:27.934][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:27.935][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:27.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:27.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:27.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:27.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:27.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:27.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:27.957][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.TRACE[2024-06-10 13:08:27.960][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.961][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.962][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:27.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:27.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.964][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:27.965][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:27.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.965][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.966][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:27.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:27.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.968][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:27.968][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:27.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.969][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.970][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:27.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:27.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.972][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:27.972][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:27.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.973][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:27.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:27.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.975][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.976][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.976][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:27.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.978][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:27.979][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:27.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.979][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.980][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:27.980][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.981][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.981][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:27.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:27.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.983][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.983][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.984][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:27.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.986][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:27.986][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:27.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.987][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:27.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:27.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.989][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:27.990][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:27.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.991][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.991][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:27.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:27.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.995][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:27.996][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:27.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.996][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.997][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:27.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:27.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:27.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:27.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:27.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:28.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:28.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:28.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:28.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:28.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:28.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:28.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:28.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:28.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:28.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:28.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:28.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:28.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:28.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:28.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:28.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:28.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:28.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:28.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.027][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-06-10 13:08:28.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.047][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:28.051][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:28.052][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-10 13:08:28.053][rule$waitAsNeeded] Wait 0.0252631 second(s).
biodb.TRACE[2024-06-10 13:08:28.108][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-10 13:08:28.337][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-10 13:08:28.567][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-06-10 13:08:28.568][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-10 13:08:28.569][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-10 13:08:28.574][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-10 13:08:28.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.664][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 13:08:28.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 13:08:28.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.700][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 13:08:28.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.745][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.TRACE[2024-06-10 13:08:28.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.762][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 13:08:28.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 13:08:28.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.777][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 13:08:28.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.779][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 13:08:28.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.791][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 13:08:28.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.829][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 13:08:28.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.830][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.TRACE[2024-06-10 13:08:28.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.867][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 13:08:28.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.869][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 13:08:28.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:28.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:28.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:28.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:28.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:28.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:28.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:28.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:28.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:28.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:28.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:28.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:28.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:28.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:28.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:28.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:28.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:28.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:28.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:28.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:28.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:28.995][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 13:08:28.999][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:29.000][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:29.002][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-10 13:08:29.084][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-10 13:08:29.158][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:29.160][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-06-10 13:08:29.165][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-06-10 13:08:29.168][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:29.172][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:29.172][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:29.174][private$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 13:08:29.250][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 13:08:29.320][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:29.323][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-06-10 13:08:29.327][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-06-10 13:08:29.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:29.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:29.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:29.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:29.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:29.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:29.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:29.357][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-06-10 13:08:29.358][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:29.360][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-06-10 13:08:29.361][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:29.362][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:29.363][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:29.364][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:29.364][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:29.365][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:29.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:29.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:29.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:29.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:29.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:29.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:29.378][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.DEBUG[2024-06-10 13:08:29.379][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-06-10 13:08:29.382][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:29.382][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:29.384][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-06-10 13:08:29.461][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 13:08:29.557][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:29.559][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-06-10 13:08:29.564][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-06-10 13:08:29.567][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-06-10 13:08:29.569][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:29.571][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:29.572][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:29.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:29.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:29.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:29.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:29.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:29.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:29.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:29.587][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:29.588][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:29.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.590][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:29.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:29.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.595][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:29.596][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:29.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.598][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.599][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:29.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:29.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.603][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:29.604][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:29.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.605][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.607][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:29.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:29.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.610][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:29.611][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:29.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.612][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.613][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:29.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:29.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.617][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:29.618][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:29.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.619][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:29.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:29.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.625][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:29.626][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:29.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.628][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.630][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:29.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:29.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.635][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:29.650][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:29.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.654][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.657][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:29.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:29.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.663][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.664][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.666][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.671][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:29.672][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:29.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.673][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:29.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:29.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.679][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:29.680][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:29.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.682][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.684][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:29.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:29.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.689][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:29.691][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:29.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.693][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:29.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:29.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:29.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:29.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:29.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:29.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:29.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:29.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:29.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:29.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:29.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:29.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:29.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:29.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:29.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:29.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:29.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:29.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:29.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:29.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:29.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:29.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:29.738][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-06-10 13:08:29.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:29.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:29.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:29.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:29.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:29.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:29.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:29.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:29.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:29.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:29.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:29.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:29.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:29.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:29.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:29.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:29.790][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 13:08:29.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:29.791][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.DEBUG[2024-06-10 13:08:29.792][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-06-10 13:08:29.793][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:29.795][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-06-10 13:08:29.796][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:29.797][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:29.798][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:29.799][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:29.800][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:29.801][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:29.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:29.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:29.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:29.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:29.812][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 13:08:29.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:29.813][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 13:08:29.815][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-06-10 13:08:29.818][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:29.819][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-10 13:08:29.820][rule$waitAsNeeded] Wait 0.181815 second(s).
biodb.TRACE[2024-06-10 13:08:30.153][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-06-10 13:08:30.225][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-06-10 13:08:30.296][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:30.299][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-06-10 13:08:30.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-06-10 13:08:30.307][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-06-10 13:08:30.309][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:30.310][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:30.311][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:30.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.322][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 13:08:30.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.327][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:30.328][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:30.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.329][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:30.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:30.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.334][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:30.335][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:30.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.336][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.338][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:30.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:30.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.341][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:30.342][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:30.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.343][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.344][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:30.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:30.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.348][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:30.348][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:30.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.350][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:30.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:30.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.361][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:30.366][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:30.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.368][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:30.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:30.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.374][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:30.376][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:30.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.379][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:30.380][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:30.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.382][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.384][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:30.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:30.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.388][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.389][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.391][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.397][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:30.398][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:30.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.399][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:30.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:30.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.405][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:30.405][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:30.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.407][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.409][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:30.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:30.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.414][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:30.415][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:30.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.416][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.417][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:30.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:30.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:30.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:30.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:30.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:30.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:30.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:30.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:30.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:30.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:30.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:30.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:30.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:30.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:30.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:30.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:30.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:30.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:30.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:30.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:30.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:30.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.454][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-06-10 13:08:30.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.495][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:30.499][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:30.500][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 13:08:30.502][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:30.503][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-10 13:08:30.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.565][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:30.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:30.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:30.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:30.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:30.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:30.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:30.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:30.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:30.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:30.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:30.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.223][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:31.227][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:31.229][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-10 13:08:31.230][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:31.231][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-10 13:08:31.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:31.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:31.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.681][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 13:08:31.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 13:08:31.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 13:08:31.693][biodb::testThat]
biodb.INFO [2024-06-10 13:08:31.694][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-10 13:08:31.695][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:31.696][biodb::testThat]
biodb.TRACE[2024-06-10 13:08:31.699][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 13:08:31.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 13:08:31.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:31.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:31.731][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:31.735][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:31.736][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:31.738][private$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 13:08:31.811][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 13:08:31.883][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:31.886][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-10 13:08:31.890][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-10 13:08:31.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:31.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:31.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:31.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:31.901][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 13:08:31.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:31.902][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 13:08:31.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:31.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:31.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:31.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:31.914][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 13:08:31.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:31.918][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:31.920][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-10 13:08:31.993][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-10 13:08:32.066][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:32.068][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-10 13:08:32.072][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-10 13:08:32.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:32.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:32.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:32.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:32.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:32.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:32.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:32.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:32.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:32.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:32.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:32.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:32.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:32.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:32.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:32.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:32.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:32.129][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 13:08:32.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:32.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:32.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:32.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:32.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:32.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:32.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:32.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.149][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.149][private$selectFields]
biodb.TRACE[2024-06-10 13:08:32.150][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:32.151][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:32.152][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.153][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.154][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.155][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.156][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.157][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.158][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.159][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.160][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.160][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.161][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.163][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.164][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:32.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.183][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-10 13:08:32.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:32.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:32.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:32.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:32.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:32.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:32.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:32.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.202][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.202][private$selectFields]
biodb.TRACE[2024-06-10 13:08:32.203][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:32.204][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:32.205][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.206][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.208][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.209][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.209][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.211][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.212][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.213][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.213][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.214][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.217][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.217][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:32.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.229][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 13:08:32.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:32.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:32.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:32.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:32.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:32.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:32.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:32.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.248][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.249][private$selectFields]
biodb.TRACE[2024-06-10 13:08:32.249][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:32.250][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:32.251][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.252][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.252][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.254][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.255][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.256][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.257][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.258][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.259][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:32.259][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.260][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.262][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.263][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:32.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:32.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.273][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-10 13:08:32.274][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 13:08:32.275][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 13:08:32.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:32.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:32.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:32.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:32.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:32.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:32.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:32.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:32.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:32.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:32.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:32.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:32.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:32.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:32.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:32.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:32.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:32.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:32.364][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:32.368][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:32.369][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:32.370][private$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 13:08:32.444][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 13:08:32.520][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:32.522][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-06-10 13:08:32.527][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-06-10 13:08:32.531][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 13:08:32.534][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:32.535][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-10 13:08:32.536][rule$waitAsNeeded] Wait 0.201293 second(s).
biodb.TRACE[2024-06-10 13:08:32.889][private$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 13:08:32.961][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 13:08:33.039][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:33.042][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-06-10 13:08:33.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-06-10 13:08:33.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.061][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.TRACE[2024-06-10 13:08:33.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.094][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 13:08:33.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.095][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 13:08:33.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.115][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 13:08:33.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.151][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 13:08:33.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.194][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.195][private$selectFields]
biodb.TRACE[2024-06-10 13:08:33.196][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:33.197][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:33.197][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.198][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.199][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.201][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.202][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.202][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.204][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.205][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.206][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.206][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.207][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.209][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.210][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:33.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.221][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-10 13:08:33.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.230][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.271][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.272][private$selectFields]
biodb.TRACE[2024-06-10 13:08:33.273][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:33.273][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:33.274][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.275][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.276][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.278][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.278][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.279][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.281][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.282][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.292][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.293][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.294][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.296][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.296][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:33.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.308][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 13:08:33.309][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.317][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 13:08:33.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.319][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 13:08:33.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.326][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.327][private$selectFields]
biodb.TRACE[2024-06-10 13:08:33.328][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:33.329][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:33.329][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.330][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.331][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.333][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.334][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.334][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.336][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.337][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.338][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.338][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.339][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.341][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.341][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:33.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.352][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-10 13:08:33.353][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 13:08:33.354][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 13:08:33.363][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 13:08:33.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 13:08:33.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 13:08:33.370][biodb::testThat]
biodb.INFO [2024-06-10 13:08:33.371][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-10 13:08:33.372][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:33.373][biodb::testThat]
biodb.TRACE[2024-06-10 13:08:33.376][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 13:08:33.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 13:08:33.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:33.414][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 13:08:33.417][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:33.418][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-10 13:08:33.420][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:33.421][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 13:08:33.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.444][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 13:08:33.447][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:33.449][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-10 13:08:33.450][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:33.451][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 13:08:33.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.483][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.TRACE[2024-06-10 13:08:33.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.494][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 13:08:33.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.503][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 13:08:33.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.513][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.513][private$selectFields]
biodb.TRACE[2024-06-10 13:08:33.514][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:33.515][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:33.516][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.516][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.517][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.519][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.520][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.522][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.523][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.523][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.524][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.525][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.526][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.527][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:33.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.538][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-10 13:08:33.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.557][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.557][private$selectFields]
biodb.TRACE[2024-06-10 13:08:33.558][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:33.559][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:33.560][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.561][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.562][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.563][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.564][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.565][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.566][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.567][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.568][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.569][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.570][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.571][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.572][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:33.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.584][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 13:08:33.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.603][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.604][private$selectFields]
biodb.TRACE[2024-06-10 13:08:33.605][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:33.606][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:33.607][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.607][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.608][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.610][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.611][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.612][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.613][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.614][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.615][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.616][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.616][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.618][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.619][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:33.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.630][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-10 13:08:33.631][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 13:08:33.632][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 13:08:33.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.667][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 13:08:33.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:33.672][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 13:08:33.676][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:33.677][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-10 13:08:33.678][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:33.680][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 13:08:33.683][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 13:08:33.686][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:33.688][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-10 13:08:33.689][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:33.690][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 13:08:33.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.750][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 13:08:33.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:33.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.763][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 13:08:33.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.780][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.781][private$selectFields]
biodb.TRACE[2024-06-10 13:08:33.781][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:33.782][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:33.783][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.784][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.785][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.786][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.787][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.788][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.789][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.790][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.791][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.791][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.792][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.794][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.794][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:33.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.805][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-10 13:08:33.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.822][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.823][private$selectFields]
biodb.TRACE[2024-06-10 13:08:33.824][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:33.825][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:33.826][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.826][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.827][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.829][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.830][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.830][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.832][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.833][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.833][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.834][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.835][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.836][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.837][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:33.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.848][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 13:08:33.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.856][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 13:08:33.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.867][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.868][private$selectFields]
biodb.TRACE[2024-06-10 13:08:33.869][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:33.869][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:33.870][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.871][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.872][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.873][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.874][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.875][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.877][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.878][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.880][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:33.880][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.881][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.883][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.884][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:33.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:33.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.897][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-10 13:08:33.898][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 13:08:33.899][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 13:08:33.909][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 13:08:33.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 13:08:33.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 13:08:33.917][biodb::testThat]
biodb.INFO [2024-06-10 13:08:33.918][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-10 13:08:33.919][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:33.920][biodb::testThat]
biodb.TRACE[2024-06-10 13:08:33.923][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-10 13:08:33.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-10 13:08:33.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.957][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 13:08:33.960][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 13:08:33.964][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:33.965][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-10 13:08:33.967][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:33.968][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 13:08:33.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:33.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:33.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:33.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:33.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:33.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:33.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:33.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:33.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:33.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:33.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:33.994][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 13:08:33.997][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:33.998][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-10 13:08:33.999][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:34.001][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 13:08:34.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:34.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:34.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.032][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.TRACE[2024-06-10 13:08:34.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:34.050][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 13:08:34.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:34.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.067][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.068][private$selectFields]
biodb.TRACE[2024-06-10 13:08:34.069][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:34.070][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:34.070][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.071][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.072][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.073][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.074][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.075][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.076][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.077][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.078][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.078][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.079][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.081][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.081][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:34.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.092][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-10 13:08:34.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:34.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.109][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.110][private$selectFields]
biodb.TRACE[2024-06-10 13:08:34.110][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:34.111][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:34.112][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.113][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.113][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.115][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.116][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.116][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.118][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.119][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.119][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.120][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.121][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.122][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.123][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:34.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.134][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 13:08:34.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.144][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 13:08:34.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.151][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.152][private$selectFields]
biodb.TRACE[2024-06-10 13:08:34.153][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:34.154][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:34.154][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.155][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.156][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.158][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.158][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.159][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.161][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.161][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.162][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.163][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.164][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.165][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.166][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:34.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.176][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-10 13:08:34.177][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 13:08:34.178][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 13:08:34.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:34.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:34.225][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 13:08:34.229][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:34.230][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-10 13:08:34.231][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:34.232][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 13:08:34.235][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 13:08:34.238][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:34.239][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-10 13:08:34.241][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:34.243][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 13:08:34.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:34.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:34.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.274][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 13:08:34.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 13:08:34.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:34.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:34.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:34.306][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-10 13:08:34.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:34.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.323][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.324][private$selectFields]
biodb.TRACE[2024-06-10 13:08:34.325][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:34.325][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:34.326][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.327][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.328][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.329][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.330][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.331][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.332][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.333][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.334][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.335][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.335][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.337][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.338][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:34.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.355][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-10 13:08:34.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:34.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.372][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.373][private$selectFields]
biodb.TRACE[2024-06-10 13:08:34.373][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:34.374][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:34.375][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.376][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.376][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.379][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.379][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.381][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.382][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.382][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.383][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.384][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.385][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.386][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:34.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.396][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-10 13:08:34.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.406][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 13:08:34.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.413][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.414][private$selectFields]
biodb.TRACE[2024-06-10 13:08:34.415][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-10 13:08:34.416][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-10 13:08:34.416][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.417][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.418][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.419][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.420][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.421][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.422][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.423][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.424][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-10 13:08:34.425][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.426][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.427][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.428][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-10 13:08:34.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.438][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-10 13:08:34.439][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-10 13:08:34.440][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-10 13:08:34.459][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-10 13:08:34.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-10 13:08:34.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-10 13:08:34.466][biodb::testThat]
biodb.INFO [2024-06-10 13:08:34.466][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-10 13:08:34.467][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:34.468][biodb::testThat]
biodb.DEBUG[2024-06-10 13:08:34.470][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-10 13:08:34.470][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:34.472][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-10 13:08:34.473][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:34.474][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:34.475][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:34.476][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:34.477][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:34.477][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:34.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.487][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 13:08:34.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:34.490][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-06-10 13:08:34.493][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:34.493][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:34.495][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-06-10 13:08:34.576][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 13:08:34.654][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:34.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-06-10 13:08:34.660][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-06-10 13:08:34.663][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-06-10 13:08:34.664][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:34.665][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:34.666][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:34.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:34.679][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:34.680][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:34.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.681][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:34.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:34.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.686][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:34.687][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:34.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.688][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.689][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:34.690][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:34.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.692][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.693][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:34.694][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:34.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.695][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.696][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:34.697][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:34.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.698][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.699][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:34.700][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:34.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.702][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.703][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:34.703][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:34.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.705][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.706][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.707][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:34.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.708][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.709][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:34.710][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:34.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.711][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.713][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:34.713][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:34.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.715][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.716][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:34.717][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:34.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.718][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:34.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:34.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:34.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:34.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:34.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:34.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:34.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:34.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:34.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:34.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:34.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:34.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:34.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:34.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:34.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:34.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:34.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:34.751][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-06-10 13:08:34.751][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-10 13:08:34.760][biodb::testThat]
biodb.INFO [2024-06-10 13:08:34.761][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-10 13:08:34.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:34.763][biodb::testThat]
biodb.DEBUG[2024-06-10 13:08:34.774][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-06-10 13:08:34.775][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-06-10 13:08:34.776][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-06-10 13:08:34.778][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-06-10 13:08:34.779][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-06-10 13:08:34.780][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:34.781][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:34.782][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:34.783][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:34.784][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:34.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:34.799][scheduler$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 13:08:34.802][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:34.803][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:34.805][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-06-10 13:08:34.877][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-06-10 13:08:34.959][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:34.961][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-06-10 13:08:34.965][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-06-10 13:08:34.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:34.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:34.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:34.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:34.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:34.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:34.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:34.976][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-06-10 13:08:34.979][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:34.980][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:34.981][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-06-10 13:08:35.056][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 13:08:35.133][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:35.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-06-10 13:08:35.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-06-10 13:08:35.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:35.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:35.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:35.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:35.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:35.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:35.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:35.152][scheduler$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 13:08:35.155][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:35.156][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-10 13:08:35.157][rule$waitAsNeeded] Wait 0.337694 second(s).
biodb.TRACE[2024-06-10 13:08:35.646][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-06-10 13:08:35.722][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 13:08:35.795][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:35.798][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-06-10 13:08:35.802][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-06-10 13:08:35.804][private$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 13:08:35.806][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:35.808][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-06-10 13:08:35.809][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:35.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:35.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:35.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:35.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:35.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:35.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:35.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:35.822][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.823][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.825][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.829][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:35.830][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:35.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.832][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.833][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:35.834][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:35.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.835][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.836][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:35.837][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:35.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.839][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.840][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:35.841][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:35.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.842][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.843][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:35.844][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:35.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.846][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.847][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:35.847][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:35.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.849][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.850][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:35.851][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:35.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.852][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.853][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:35.854][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:35.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.856][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.857][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:35.859][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:35.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.861][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.862][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:35.863][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:35.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.865][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:35.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:35.891][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:35.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:35.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:35.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:35.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:35.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:35.902][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.904][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.905][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.910][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:35.911][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:35.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.912][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.914][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:35.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:35.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.918][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:35.919][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:35.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.920][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.922][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:35.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:35.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.925][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:35.926][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:35.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.927][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:35.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:35.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.932][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:35.933][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:35.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.934][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:35.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:35.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.939][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:35.940][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:35.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.941][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.942][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:35.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:35.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.946][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:35.947][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:35.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.948][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.949][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:35.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:35.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.953][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:35.954][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:35.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.955][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:35.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:35.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.960][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:35.961][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:35.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.963][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:35.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:35.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.968][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:35.968][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:35.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.971][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:35.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:35.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.974][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:35.975][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:35.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.977][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.978][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:35.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:35.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:35.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:35.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:35.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:35.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:35.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:36.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:36.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:36.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:36.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:36.017][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.018][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.021][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.027][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:36.028][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:36.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.029][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.031][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:36.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:36.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.034][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:36.035][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:36.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.037][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:36.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:36.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.041][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:36.042][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:36.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.044][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:36.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:36.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.048][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:36.049][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:36.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.050][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.052][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:36.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:36.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.055][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:36.056][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:36.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.057][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.073][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:36.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:36.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.077][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:36.078][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:36.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.080][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.081][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:36.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:36.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.085][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:36.085][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:36.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.087][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:36.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:36.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.092][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:36.092][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:36.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.094][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:36.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:36.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.099][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:36.100][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:36.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.101][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.102][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:36.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:36.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.106][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:36.107][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:36.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.108][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.109][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:36.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:36.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:36.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:36.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:36.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:36.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:36.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:36.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:36.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:36.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:36.164][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-06-10 13:08:36.165][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-10 13:08:36.166][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-06-10 13:08:36.179][biodb::testThat]
biodb.INFO [2024-06-10 13:08:36.180][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-10 13:08:36.181][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:36.182][biodb::testThat]
biodb.INFO [2024-06-10 13:08:36.204][biodb::testThat]
biodb.INFO [2024-06-10 13:08:36.205][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-10 13:08:36.206][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:36.207][biodb::testThat]
biodb.INFO [2024-06-10 13:08:36.214][biodb::testThat]
biodb.INFO [2024-06-10 13:08:36.215][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-10 13:08:36.216][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:36.217][biodb::testThat]
biodb.DEBUG[2024-06-10 13:08:36.219][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:36.222][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:36.223][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:36.225][private$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 13:08:36.357][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 13:08:36.537][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:36.539][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-06-10 13:08:36.543][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-06-10 13:08:36.555][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:36.556][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:36.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.557][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:36.558][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:36.559][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:36.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:36.561][ef$get] fields variable is a list.
biodb.INFO [2024-06-10 13:08:36.562][biodb::testThat]
biodb.INFO [2024-06-10 13:08:36.563][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-10 13:08:36.564][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:36.565][biodb::testThat]
biodb.ERROR[2024-06-10 13:08:36.577][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-10 13:08:36.593][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-10 13:08:36.606][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 13:08:36.607][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-10 13:08:36.608][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-10 13:08:36.609][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 13:08:36.609][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:36.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:36.611][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.612][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-10 13:08:36.623][biodb::testContext]
biodb.INFO [2024-06-10 13:08:36.624][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 13:08:36.625][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-06-10 13:08:36.626][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 13:08:36.626][biodb::testContext]
biodb.INFO [2024-06-10 13:08:36.628][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-10 13:08:36.630][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 13:08:36.635][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:36.636][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 13:08:36.637][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 13:08:36.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.640][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 13:08:36.641][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 13:08:36.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.643][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 13:08:36.644][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 13:08:36.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.647][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 13:08:36.648][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 13:08:36.649][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 13:08:36.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.651][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 13:08:36.651][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 13:08:36.652][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 13:08:36.653][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 13:08:36.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.656][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 13:08:36.657][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 13:08:36.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.659][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 13:08:36.660][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 13:08:36.661][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 13:08:36.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.664][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 13:08:36.665][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 13:08:36.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.668][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 13:08:36.668][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 13:08:36.669][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 13:08:36.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.672][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 13:08:36.673][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 13:08:36.673][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 13:08:36.674][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 13:08:36.675][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 13:08:36.676][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 13:08:36.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.678][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 13:08:36.679][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 13:08:36.680][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 13:08:36.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.693][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 13:08:36.694][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 13:08:36.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.696][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 13:08:36.697][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 13:08:36.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.700][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 13:08:36.701][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 13:08:36.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.704][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 13:08:36.704][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 13:08:36.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.707][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 13:08:36.708][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 13:08:36.721][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 13:08:36.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.723][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.DEBUG[2024-06-10 13:08:36.724][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 13:08:36.725][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 13:08:36.726][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 13:08:36.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.729][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 13:08:36.731][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.731][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-10 13:08:36.732][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.733][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:36.734][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.735][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.735][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.736][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.737][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 13:08:36.738][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:36.739][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.739][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 13:08:36.740][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:36.741][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.742][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.742][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:36.742][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:36.742][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:36.742][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 13:08:36.742][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 13:08:36.743][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:36.744][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:36.745][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:36.745][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:36.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:36.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:36.748][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.748][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.749][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:36.750][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:36.751][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.751][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.752][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 13:08:36.754][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.755][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 13:08:36.755][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.756][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:36.757][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.758][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.758][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.759][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.760][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 13:08:36.761][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:36.761][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.762][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 13:08:36.763][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:36.764][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.764][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.765][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:36.765][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:36.765][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:36.765][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 13:08:36.765][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 13:08:36.766][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:36.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:36.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:36.768][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:36.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:36.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:36.770][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.771][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:36.773][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:36.773][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.774][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.775][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 13:08:36.776][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.777][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-10 13:08:36.778][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.779][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:36.780][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.780][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.781][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.782][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.783][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 13:08:36.783][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:36.784][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.785][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 13:08:36.786][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:36.787][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.787][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.788][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.789][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:36.790][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:36.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:36.791][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:36.792][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:36.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:36.793][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.794][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.795][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:36.796][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:36.796][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.797][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.798][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 13:08:36.800][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.801][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 13:08:36.801][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.802][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:36.803][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.804][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.804][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.805][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.806][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 13:08:36.807][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:36.808][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.808][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 13:08:36.809][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:36.810][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.811][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:36.812][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.812][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:36.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:36.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:36.814][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:36.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:36.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:36.817][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:36.817][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.818][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:36.819][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:36.820][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:36.820][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:36.821][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:36.822][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.825][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 13:08:36.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.830][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 13:08:36.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.835][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 13:08:36.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.837][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 13:08:36.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.840][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 13:08:36.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.843][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 13:08:36.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.845][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 13:08:36.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.853][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 13:08:36.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.856][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 13:08:36.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.857][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 13:08:36.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.864][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 13:08:36.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.872][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 13:08:36.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.881][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 13:08:36.882][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 13:08:36.884][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 13:08:36.885][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 13:08:36.886][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 13:08:36.887][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 13:08:36.888][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 13:08:36.889][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 13:08:36.890][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 13:08:36.891][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 13:08:36.893][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 13:08:36.894][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 13:08:36.895][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 13:08:36.896][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 13:08:36.897][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 13:08:36.898][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 13:08:36.899][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 13:08:36.900][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 13:08:36.902][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 13:08:36.904][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 13:08:36.905][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 13:08:36.906][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 13:08:36.908][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 13:08:36.909][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 13:08:36.910][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 13:08:36.912][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 13:08:36.913][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 13:08:36.914][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 13:08:36.916][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 13:08:36.917][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 13:08:36.918][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 13:08:36.919][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 13:08:36.921][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 13:08:36.922][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 13:08:36.923][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 13:08:36.924][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 13:08:36.925][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 13:08:36.927][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 13:08:36.928][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 13:08:36.929][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 13:08:36.930][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 13:08:36.931][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 13:08:36.933][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 13:08:36.934][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 13:08:36.935][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 13:08:36.936][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 13:08:36.938][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 13:08:36.939][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 13:08:36.940][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 13:08:36.941][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 13:08:36.942][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 13:08:36.944][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 13:08:36.945][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 13:08:36.946][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 13:08:36.947][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 13:08:36.948][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 13:08:36.949][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 13:08:36.950][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 13:08:36.952][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 13:08:36.953][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 13:08:36.954][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 13:08:36.955][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 13:08:36.956][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 13:08:36.957][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 13:08:36.958][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 13:08:36.960][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 13:08:36.961][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 13:08:36.962][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 13:08:36.963][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 13:08:36.972][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 13:08:36.973][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 13:08:36.974][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 13:08:36.975][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 13:08:36.976][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 13:08:36.978][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 13:08:36.979][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 13:08:36.980][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 13:08:36.981][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 13:08:36.982][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 13:08:36.984][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 13:08:36.985][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 13:08:36.986][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 13:08:36.987][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 13:08:36.989][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 13:08:36.991][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-10 13:08:36.992][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:36.993][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:36.994][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:36.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:36.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:36.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:36.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:36.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:36.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.004][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 13:08:37.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.020][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 13:08:37.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.023][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 13:08:37.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.028][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 13:08:37.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.030][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 13:08:37.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.038][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 13:08:37.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.043][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 13:08:37.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.050][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 13:08:37.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.058][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 13:08:37.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.060][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 13:08:37.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.063][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 13:08:37.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.066][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 13:08:37.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.070][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 13:08:37.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.071][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 13:08:37.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.075][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 13:08:37.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.076][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 13:08:37.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:37.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.080][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 13:08:37.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.085][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-10 13:08:37.087][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-10 13:08:37.089][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:37.090][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 13:08:37.091][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:37.092][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:37.093][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:37.094][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:37.095][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:37.096][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-10 13:08:37.097][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-10 13:08:37.097][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:37.098][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:37.099][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-10 13:08:37.100][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:37.101][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-10 13:08:37.101][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-10 13:08:37.101][self$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 13:08:37.101][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-10 13:08:37.101][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-10 13:08:37.101][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-10 13:08:37.101][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-10 13:08:37.101][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-10 13:08:37.101][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-10 13:08:37.101][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-10 13:08:37.101][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-10 13:08:37.102][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:37.103][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:37.103][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:37.103][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:37.104][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-10 13:08:37.105][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:37.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:37.106][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:37.107][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:37.108][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:37.108][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:37.109][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:37.109][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-10 13:08:37.110][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:37.111][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:37.112][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:37.113][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-10 13:08:37.113][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-10 13:08:37.114][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 13:08:37.115][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 13:08:37.117][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-10 13:08:37.118][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 13:08:37.119][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 13:08:37.121][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 13:08:37.124][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-10 13:08:37.125][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-10 13:08:37.126][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-10 13:08:37.128][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-10 13:08:37.129][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 13:08:37.130][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 13:08:37.131][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-10 13:08:37.132][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-10 13:08:37.133][biodb::testThat]
biodb.INFO [2024-06-10 13:08:37.134][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-06-10 13:08:37.135][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:37.136][biodb::testThat]
biodb.DEBUG[2024-06-10 13:08:37.140][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 13:08:37.144][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:37.145][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:37.146][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-06-10 13:08:37.214][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-06-10 13:08:37.298][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:37.300][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-06-10 13:08:37.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-06-10 13:08:37.308][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:37.311][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:37.312][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:37.314][private$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 13:08:37.389][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 13:08:37.459][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:37.462][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-06-10 13:08:37.466][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-06-10 13:08:37.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:37.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.482][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 13:08:37.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:37.487][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:37.488][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-10 13:08:37.572][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-10 13:08:37.651][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:37.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-06-10 13:08:37.658][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 13:08:37.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:37.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:37.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.699][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:37.703][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:37.704][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-10 13:08:37.705][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:37.706][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-10 13:08:37.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:37.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.718][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:37.722][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:37.723][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-10 13:08:37.724][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:37.725][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 13:08:37.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:37.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.735][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 13:08:37.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:37.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.759][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 13:08:37.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.764][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:37.767][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:37.768][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-10 13:08:37.769][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:37.770][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-10 13:08:37.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:37.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.783][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:37.786][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:37.787][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-10 13:08:37.788][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:37.789][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-10 13:08:37.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:37.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:37.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:37.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:37.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:37.800][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:37.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:37.802][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:37.805][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:37.806][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-10 13:08:37.807][rule$waitAsNeeded] Wait 0.338779 second(s).
biodb.TRACE[2024-06-10 13:08:38.298][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-10 13:08:38.369][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-10 13:08:38.444][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:38.446][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-06-10 13:08:38.449][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-06-10 13:08:38.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:38.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:38.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:38.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-10 13:08:38.459][biodb::testThat]
biodb.INFO [2024-06-10 13:08:38.459][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-06-10 13:08:38.460][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:38.460][biodb::testThat]
biodb.DEBUG[2024-06-10 13:08:38.462][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:38.464][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:38.465][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:38.466][private$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 13:08:38.536][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 13:08:38.601][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:38.603][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-06-10 13:08:38.606][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-06-10 13:08:38.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:38.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:38.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:38.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.619][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 13:08:38.623][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:38.624][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:38.626][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-10 13:08:38.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-10 13:08:38.760][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:38.762][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-06-10 13:08:38.764][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-06-10 13:08:38.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:38.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:38.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:38.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-10 13:08:38.776][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 13:08:38.777][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-10 13:08:38.778][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-10 13:08:38.778][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 13:08:38.778][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:38.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:38.779][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.781][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-10 13:08:38.783][biodb::testContext]
biodb.INFO [2024-06-10 13:08:38.783][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 13:08:38.784][biodb::testContext] Test context - Test web services
biodb.INFO [2024-06-10 13:08:38.784][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 13:08:38.785][biodb::testContext]
biodb.INFO [2024-06-10 13:08:38.786][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-10 13:08:38.787][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 13:08:38.790][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:38.791][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 13:08:38.791][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 13:08:38.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.792][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 13:08:38.792][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 13:08:38.793][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 13:08:38.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.796][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 13:08:38.797][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 13:08:38.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.799][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 13:08:38.799][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 13:08:38.799][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 13:08:38.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.801][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 13:08:38.802][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 13:08:38.802][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 13:08:38.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.806][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 13:08:38.807][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 13:08:38.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.810][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 13:08:38.810][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 13:08:38.810][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 13:08:38.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.811][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 13:08:38.812][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 13:08:38.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.813][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 13:08:38.813][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 13:08:38.814][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 13:08:38.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.815][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 13:08:38.815][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 13:08:38.816][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 13:08:38.817][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 13:08:38.817][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 13:08:38.818][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 13:08:38.818][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 13:08:38.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.820][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 13:08:38.820][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 13:08:38.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.821][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 13:08:38.821][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 13:08:38.822][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 13:08:38.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.823][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 13:08:38.823][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 13:08:38.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.825][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 13:08:38.825][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 13:08:38.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.826][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 13:08:38.827][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 13:08:38.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.828][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 13:08:38.828][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 13:08:38.828][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 13:08:38.838][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 13:08:38.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.841][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 13:08:38.842][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 13:08:38.842][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 13:08:38.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.843][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 13:08:38.844][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 13:08:38.844][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.845][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-10 13:08:38.846][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.846][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:38.847][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.847][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.847][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.848][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.848][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 13:08:38.848][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:38.849][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.849][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 13:08:38.849][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:38.850][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.850][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.850][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:38.850][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:38.850][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:38.850][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 13:08:38.850][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 13:08:38.851][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:38.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:38.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:38.852][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:38.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:38.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:38.853][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.853][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.853][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:38.854][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:38.854][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.855][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.855][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 13:08:38.856][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.857][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 13:08:38.857][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.858][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:38.858][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.858][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.859][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.859][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.859][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 13:08:38.860][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:38.860][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.861][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 13:08:38.861][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:38.861][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.862][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.862][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:38.862][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:38.862][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:38.862][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 13:08:38.862][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 13:08:38.862][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:38.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:38.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:38.865][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:38.866][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:38.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:38.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.868][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.869][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:38.870][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:38.871][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.872][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.873][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 13:08:38.875][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.875][self$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 13:08:38.876][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.876][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:38.876][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.877][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.877][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.891][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.892][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 13:08:38.893][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:38.893][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.893][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 13:08:38.894][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:38.895][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.896][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.897][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.897][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:38.898][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:38.899][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:38.900][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:38.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:38.901][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:38.902][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.903][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.903][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:38.904][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:38.905][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.905][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.906][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 13:08:38.907][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.908][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 13:08:38.909][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.910][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:38.911][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.912][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.912][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.913][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.914][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 13:08:38.915][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:38.916][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.916][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 13:08:38.917][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:38.918][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.919][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:38.920][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.920][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:38.921][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:38.922][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:38.923][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:38.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:38.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:38.925][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:38.925][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.925][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:38.926][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:38.926][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:38.926][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:38.927][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:38.927][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.941][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 13:08:38.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.942][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.DEBUG[2024-06-10 13:08:38.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.943][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 13:08:38.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.944][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 13:08:38.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.945][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.DEBUG[2024-06-10 13:08:38.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.946][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 13:08:38.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.950][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 13:08:38.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.952][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.DEBUG[2024-06-10 13:08:38.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.957][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 13:08:38.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:38.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:38.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:38.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:38.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:38.960][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 13:08:38.960][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 13:08:38.961][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 13:08:38.962][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 13:08:38.963][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 13:08:38.963][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 13:08:38.964][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 13:08:38.964][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 13:08:38.965][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 13:08:38.965][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 13:08:38.966][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 13:08:38.966][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 13:08:38.967][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 13:08:38.967][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 13:08:38.968][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 13:08:38.968][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 13:08:38.969][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 13:08:38.970][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 13:08:38.970][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 13:08:38.971][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 13:08:38.971][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 13:08:38.972][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 13:08:38.972][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 13:08:38.973][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 13:08:38.973][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 13:08:38.974][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 13:08:38.974][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 13:08:38.976][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 13:08:38.977][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 13:08:38.978][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 13:08:38.978][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 13:08:38.979][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 13:08:38.980][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 13:08:38.982][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 13:08:38.983][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 13:08:38.985][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 13:08:38.986][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 13:08:38.987][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 13:08:38.988][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 13:08:38.989][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 13:08:38.991][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 13:08:38.992][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 13:08:38.993][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 13:08:38.994][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 13:08:38.995][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 13:08:38.996][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 13:08:38.997][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 13:08:38.997][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 13:08:38.999][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 13:08:39.000][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 13:08:39.001][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 13:08:39.003][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 13:08:39.004][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 13:08:39.005][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 13:08:39.006][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 13:08:39.007][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 13:08:39.008][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 13:08:39.010][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 13:08:39.011][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 13:08:39.013][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 13:08:39.014][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 13:08:39.015][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 13:08:39.016][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 13:08:39.017][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 13:08:39.018][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 13:08:39.019][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 13:08:39.020][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 13:08:39.020][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 13:08:39.021][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 13:08:39.023][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 13:08:39.024][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 13:08:39.026][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 13:08:39.027][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 13:08:39.029][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 13:08:39.030][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 13:08:39.031][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 13:08:39.032][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 13:08:39.033][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 13:08:39.035][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 13:08:39.036][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 13:08:39.037][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 13:08:39.038][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 13:08:39.039][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 13:08:39.041][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 13:08:39.043][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-10 13:08:39.044][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:39.044][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.045][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.046][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 13:08:39.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.050][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 13:08:39.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.060][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 13:08:39.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.061][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 13:08:39.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.066][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 13:08:39.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.070][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 13:08:39.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.076][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 13:08:39.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.080][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 13:08:39.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.117][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.DEBUG[2024-06-10 13:08:39.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.122][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 13:08:39.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.130][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 13:08:39.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.135][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 13:08:39.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.145][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-10 13:08:39.146][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-10 13:08:39.148][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.149][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.150][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.151][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:39.152][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.153][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.153][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.154][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-10 13:08:39.155][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-10 13:08:39.156][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:39.156][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.157][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-10 13:08:39.158][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-10 13:08:39.159][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-10 13:08:39.160][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.161][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:39.161][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:39.161][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:39.162][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-10 13:08:39.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.164][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:39.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.166][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.167][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:39.167][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-10 13:08:39.168][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:39.168][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:39.169][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.170][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-10 13:08:39.170][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-10 13:08:39.171][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 13:08:39.173][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 13:08:39.174][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-10 13:08:39.176][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 13:08:39.177][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 13:08:39.178][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 13:08:39.182][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-10 13:08:39.183][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-10 13:08:39.184][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-10 13:08:39.186][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-10 13:08:39.187][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 13:08:39.188][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 13:08:39.189][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-10 13:08:39.190][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-10 13:08:39.192][biodb::testThat]
biodb.INFO [2024-06-10 13:08:39.192][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-06-10 13:08:39.193][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:39.194][biodb::testThat]
biodb.DEBUG[2024-06-10 13:08:39.197][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-10 13:08:39.201][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:39.203][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-10 13:08:39.204][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:39.205][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-10 13:08:39.209][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-10 13:08:39.212][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:39.213][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:39.215][private$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 13:08:39.301][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 13:08:39.374][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:39.377][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-06-10 13:08:39.381][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-06-10 13:08:39.390][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 13:08:39.391][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-10 13:08:39.392][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-10 13:08:39.393][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 13:08:39.394][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.395][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.397][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.397][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.INFO [2024-06-10 13:08:39.401][biodb::testContext]
biodb.INFO [2024-06-10 13:08:39.402][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 13:08:39.403][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-06-10 13:08:39.404][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-10 13:08:39.404][biodb::testContext]
biodb.INFO [2024-06-10 13:08:39.406][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-10 13:08:39.408][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-10 13:08:39.413][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:39.414][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-10 13:08:39.415][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-10 13:08:39.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.418][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-10 13:08:39.418][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-10 13:08:39.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.421][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-10 13:08:39.422][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-10 13:08:39.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.425][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-10 13:08:39.426][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-10 13:08:39.427][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-10 13:08:39.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.430][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-10 13:08:39.430][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-10 13:08:39.431][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-10 13:08:39.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.434][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-10 13:08:39.435][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-10 13:08:39.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.437][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.DEBUG[2024-06-10 13:08:39.438][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-10 13:08:39.439][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-10 13:08:39.439][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-10 13:08:39.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.442][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-10 13:08:39.443][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-10 13:08:39.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.445][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 13:08:39.446][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-10 13:08:39.447][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-10 13:08:39.447][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-10 13:08:39.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.450][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-10 13:08:39.451][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-10 13:08:39.452][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-10 13:08:39.453][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-10 13:08:39.453][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-10 13:08:39.454][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-10 13:08:39.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.457][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-10 13:08:39.458][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-10 13:08:39.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.461][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-10 13:08:39.461][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-10 13:08:39.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.464][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-10 13:08:39.466][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-10 13:08:39.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.470][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-10 13:08:39.471][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-10 13:08:39.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.473][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 13:08:39.474][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-10 13:08:39.475][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-10 13:08:39.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.478][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-10 13:08:39.479][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-10 13:08:39.493][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-10 13:08:39.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.496][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-10 13:08:39.497][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-10 13:08:39.498][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-10 13:08:39.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.501][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-10 13:08:39.503][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.504][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-10 13:08:39.505][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.505][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:39.506][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.507][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.508][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.508][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.509][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 13:08:39.510][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:39.511][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.512][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-10 13:08:39.512][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:39.513][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.514][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.515][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:39.515][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:39.515][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:39.515][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 13:08:39.515][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 13:08:39.516][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:39.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.518][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:39.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.519][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.520][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.521][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:39.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:39.523][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.524][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.525][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-10 13:08:39.526][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.527][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 13:08:39.528][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.529][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:39.530][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.530][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.531][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.532][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.533][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 13:08:39.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:39.534][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.535][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-10 13:08:39.536][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:39.537][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.537][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.538][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:39.538][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:39.538][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:39.538][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-10 13:08:39.538][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-10 13:08:39.539][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:39.540][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.541][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:39.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.543][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.544][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.545][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:39.546][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:39.546][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.547][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.548][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-10 13:08:39.550][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.551][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-10 13:08:39.552][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.552][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:39.553][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.554][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.555][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.556][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.556][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-10 13:08:39.557][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:39.558][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.559][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-10 13:08:39.560][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:39.560][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.561][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.562][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.563][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:39.564][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.565][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:39.566][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.567][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.568][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.568][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.569][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:39.577][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:39.581][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.582][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.583][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-10 13:08:39.585][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.586][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-10 13:08:39.586][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.587][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:39.588][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.589][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.589][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.590][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.591][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-10 13:08:39.592][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:39.593][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.593][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-10 13:08:39.594][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:39.595][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.596][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.597][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.597][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-10 13:08:39.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.599][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:39.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.602][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.603][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:39.604][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:39.605][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.605][self$setPropertyValue]
biodb.DEBUG[2024-06-10 13:08:39.607][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:39.607][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.610][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 13:08:39.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.612][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 13:08:39.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.639][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 13:08:39.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.667][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-10 13:08:39.668][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-10 13:08:39.669][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-10 13:08:39.671][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-10 13:08:39.672][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 13:08:39.673][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-10 13:08:39.674][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-10 13:08:39.675][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-10 13:08:39.676][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-10 13:08:39.677][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-10 13:08:39.679][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 13:08:39.680][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-10 13:08:39.681][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-10 13:08:39.682][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-10 13:08:39.683][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-10 13:08:39.684][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-10 13:08:39.685][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-10 13:08:39.686][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-10 13:08:39.687][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 13:08:39.689][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-10 13:08:39.690][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-10 13:08:39.691][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-10 13:08:39.692][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-10 13:08:39.693][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-10 13:08:39.694][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-10 13:08:39.695][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-10 13:08:39.696][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-10 13:08:39.697][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-10 13:08:39.698][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-10 13:08:39.700][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-10 13:08:39.701][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-10 13:08:39.702][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-10 13:08:39.703][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-10 13:08:39.704][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-10 13:08:39.705][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-10 13:08:39.706][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-10 13:08:39.707][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-10 13:08:39.708][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-10 13:08:39.710][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-10 13:08:39.711][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-10 13:08:39.712][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-10 13:08:39.713][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-10 13:08:39.714][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-10 13:08:39.715][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-10 13:08:39.716][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-10 13:08:39.717][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-10 13:08:39.719][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-10 13:08:39.720][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-10 13:08:39.721][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-10 13:08:39.722][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-10 13:08:39.723][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-10 13:08:39.724][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-10 13:08:39.725][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-10 13:08:39.726][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-10 13:08:39.727][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-10 13:08:39.729][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-10 13:08:39.730][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-10 13:08:39.731][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-10 13:08:39.732][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-10 13:08:39.733][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-10 13:08:39.734][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-10 13:08:39.735][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-10 13:08:39.736][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-10 13:08:39.737][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-10 13:08:39.739][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-10 13:08:39.740][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-10 13:08:39.741][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 13:08:39.742][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 13:08:39.743][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-10 13:08:39.744][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-10 13:08:39.745][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-10 13:08:39.746][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-10 13:08:39.748][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-10 13:08:39.749][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-10 13:08:39.750][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-10 13:08:39.751][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-10 13:08:39.752][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-10 13:08:39.753][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-10 13:08:39.754][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-10 13:08:39.755][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-10 13:08:39.756][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-10 13:08:39.758][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-10 13:08:39.759][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-10 13:08:39.760][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-10 13:08:39.762][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-10 13:08:39.763][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-10 13:08:39.763][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.765][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.769][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 13:08:39.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.770][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 13:08:39.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.774][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 13:08:39.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.794][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 13:08:39.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.799][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 13:08:39.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.804][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 13:08:39.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.809][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 13:08:39.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.813][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 13:08:39.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.814][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 13:08:39.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.819][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 13:08:39.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.823][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 13:08:39.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.829][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.DEBUG[2024-06-10 13:08:39.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.840][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 13:08:39.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.841][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 13:08:39.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.845][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 13:08:39.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.846][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 13:08:39.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-10 13:08:39.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.857][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 13:08:39.859][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-10 13:08:39.861][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-10 13:08:39.863][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.864][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.865][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.865][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-10 13:08:39.866][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.868][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.869][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-10 13:08:39.869][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-10 13:08:39.870][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-10 13:08:39.871][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.872][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-10 13:08:39.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-10 13:08:39.874][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-10 13:08:39.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-10 13:08:39.874][self$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 13:08:39.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-10 13:08:39.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-10 13:08:39.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-10 13:08:39.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-10 13:08:39.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-10 13:08:39.874][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-10 13:08:39.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-10 13:08:39.874][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-10 13:08:39.875][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-10 13:08:39.876][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-10 13:08:39.876][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-10 13:08:39.876][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-10 13:08:39.877][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-10 13:08:39.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.880][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-10 13:08:39.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-10 13:08:39.881][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-10 13:08:39.882][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-10 13:08:39.883][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:39.883][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-10 13:08:39.883][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-10 13:08:39.884][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-10 13:08:39.885][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-10 13:08:39.886][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-10 13:08:39.886][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-10 13:08:39.887][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-10 13:08:39.889][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-10 13:08:39.890][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-10 13:08:39.891][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-10 13:08:39.893][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-10 13:08:39.894][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-10 13:08:39.897][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-10 13:08:39.898][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-10 13:08:39.900][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-10 13:08:39.901][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-10 13:08:39.902][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 13:08:39.903][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-10 13:08:39.904][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-10 13:08:39.905][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-10 13:08:39.906][biodb::testThat]
biodb.INFO [2024-06-10 13:08:39.907][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-06-10 13:08:39.908][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-10 13:08:39.909][biodb::testThat]
biodb.DEBUG[2024-06-10 13:08:39.912][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 13:08:39.916][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:39.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-10 13:08:39.919][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:39.921][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 13:08:39.925][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 13:08:39.928][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-10 13:08:39.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-06-10 13:08:39.931][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-10 13:08:39.933][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 13:08:39.937][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-06-10 13:08:39.938][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-10 13:08:39.940][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-06-10 13:08:39.941][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-10 13:08:39.942][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-10 13:08:39.943][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-10 13:08:39.944][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-10 13:08:39.945][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-10 13:08:39.946][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-10 13:08:39.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:39.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:39.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:39.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:39.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:39.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:39.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-10 13:08:39.960][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-06-10 13:08:39.963][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-10 13:08:39.964][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-10 13:08:39.965][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-06-10 13:08:40.047][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 13:08:40.185][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-10 13:08:40.188][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-06-10 13:08:40.192][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-06-10 13:08:40.195][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-06-10 13:08:40.197][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-10 13:08:40.198][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-10 13:08:40.199][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-10 13:08:40.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-10 13:08:40.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:40.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:40.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:40.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:40.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:40.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-10 13:08:40.214][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:40.215][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:40.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.217][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:40.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:40.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.222][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:40.223][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:40.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.224][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.225][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-10 13:08:40.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-10 13:08:40.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.229][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:40.230][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:40.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.231][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.232][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-10 13:08:40.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-10 13:08:40.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.236][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-10 13:08:40.237][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-10 13:08:40.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.238][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.239][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-10 13:08:40.240][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-10 13:08:40.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.242][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.243][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:40.244][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:40.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.245][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.247][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:40.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-10 13:08:40.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.250][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:40.251][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:40.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.252][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.253][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-10 13:08:40.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-10 13:08:40.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.257][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:40.258][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:40.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.259][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:40.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-10 13:08:40.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.264][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:40.265][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:40.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.266][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-10 13:08:40.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-10 13:08:40.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.271][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:40.272][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:40.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.273][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.274][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-10 13:08:40.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-10 13:08:40.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.278][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:40.278][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:40.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.280][ef$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.281][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-10 13:08:40.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-10 13:08:40.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:40.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:40.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:40.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:40.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:40.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:40.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-10 13:08:40.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-10 13:08:40.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:40.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:40.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:40.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:40.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:40.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:40.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:40.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:40.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:40.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:40.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-10 13:08:40.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-10 13:08:40.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-10 13:08:40.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-10 13:08:40.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-10 13:08:40.316][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-06-10 13:08:40.320][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-10 13:08:40.322][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-10 13:08:40.323][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-10 13:08:40.323][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-10 13:08:40.324][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-10 13:08:40.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-10 13:08:40.326][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-10 13:08:40.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-10 13:08:40.327][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-10 13:08:40.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 17.483   1.040  26.768

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	2.424	0.643	3.202
ChebiEntry	0.404	0.015	0.421