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 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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: 1.12.0

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_1.12.0.tar.gz

StartedAt: 2024-12-20 12:37:55 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 12:39:17 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 82.6 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 [2024-12-20 12:38:46.365][biodb::testContext]
biodb.INFO [2024-12-20 12:38:46.370][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 12:38:46.371][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-12-20 12:38:46.372][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 12:38:46.373][biodb::testContext]
biodb.INFO [2024-12-20 12:38:46.382][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-12-20 12:38:46.384][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-12-20 12:38:46.397][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:38:46.399][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-12-20 12:38:46.400][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-12-20 12:38:46.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.404][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-12-20 12:38:46.424][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-12-20 12:38:46.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.428][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-12-20 12:38:46.429][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-12-20 12:38:46.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.433][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-12-20 12:38:46.448][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-12-20 12:38:46.450][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-12-20 12:38:46.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.452][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[2024-12-20 12:38:46.453][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-12-20 12:38:46.454][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-12-20 12:38:46.455][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-12-20 12:38:46.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.457][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-12-20 12:38:46.458][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-12-20 12:38:46.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.461][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-12-20 12:38:46.462][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-12-20 12:38:46.463][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-12-20 12:38:46.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.466][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-12-20 12:38:46.467][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-12-20 12:38:46.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.469][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[2024-12-20 12:38:46.470][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-12-20 12:38:46.472][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-12-20 12:38:46.473][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-12-20 12:38:46.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.476][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-12-20 12:38:46.477][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-12-20 12:38:46.478][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-12-20 12:38:46.479][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-12-20 12:38:46.480][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-12-20 12:38:46.480][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-12-20 12:38:46.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.484][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-12-20 12:38:46.485][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-12-20 12:38:46.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.488][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-12-20 12:38:46.489][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-12-20 12:38:46.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.492][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-12-20 12:38:46.493][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-12-20 12:38:46.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.496][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-12-20 12:38:46.497][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-12-20 12:38:46.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.500][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-12-20 12:38:46.501][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-12-20 12:38:46.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.504][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-12-20 12:38:46.505][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-12-20 12:38:46.521][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-12-20 12:38:46.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.525][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-12-20 12:38:46.526][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-12-20 12:38:46.527][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-12-20 12:38:46.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.534][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-12-20 12:38:46.569][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.585][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-12-20 12:38:46.587][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.588][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:38:46.588][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.589][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.590][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.591][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.592][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 12:38:46.593][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:38:46.594][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.595][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-12-20 12:38:46.597][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:38:46.597][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.598][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.600][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:38:46.600][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:38:46.600][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:38:46.600][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 12:38:46.600][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 12:38:46.601][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:38:46.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:38:46.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:38:46.604][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:38:46.605][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:38:46.605][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:38:46.606][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.607][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.608][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:38:46.608][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:38:46.609][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.610][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.611][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-12-20 12:38:46.613][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.614][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 12:38:46.614][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.615][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:38:46.616][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.617][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.618][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.619][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.619][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 12:38:46.620][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:38:46.621][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.622][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-12-20 12:38:46.623][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:38:46.624][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.624][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.625][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:38:46.625][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:38:46.625][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:38:46.625][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 12:38:46.625][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 12:38:46.626][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:38:46.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:38:46.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:38:46.629][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:38:46.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:38:46.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:38:46.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.632][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.633][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:38:46.633][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:38:46.634][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.635][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.636][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-12-20 12:38:46.637][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.638][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-12-20 12:38:46.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:38:46.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.650][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.651][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.652][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 12:38:46.653][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:38:46.654][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.654][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-12-20 12:38:46.655][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:38:46.656][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.657][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.658][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.659][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:38:46.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:38:46.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:38:46.661][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:38:46.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:38:46.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:38:46.663][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.664][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.665][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:38:46.666][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:38:46.666][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.667][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.668][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-12-20 12:38:46.670][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.671][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 12:38:46.672][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.672][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:38:46.673][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.674][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.675][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.676][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.677][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 12:38:46.678][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:38:46.679][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.679][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-12-20 12:38:46.680][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:38:46.681][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.682][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.683][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.684][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:38:46.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:38:46.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:38:46.686][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:38:46.687][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:38:46.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:38:46.688][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.689][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.690][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:38:46.691][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:38:46.692][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.693][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:38:46.698][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:38:46.699][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.729][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[2024-12-20 12:38:46.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.750][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[2024-12-20 12:38:46.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.763][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-12-20 12:38:46.769][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-12-20 12:38:46.770][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-12-20 12:38:46.771][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-12-20 12:38:46.773][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 12:38:46.774][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-12-20 12:38:46.775][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-12-20 12:38:46.776][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-12-20 12:38:46.777][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-12-20 12:38:46.778][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-12-20 12:38:46.779][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 12:38:46.781][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-12-20 12:38:46.782][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-12-20 12:38:46.783][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-12-20 12:38:46.784][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-12-20 12:38:46.785][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-12-20 12:38:46.786][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-12-20 12:38:46.788][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-12-20 12:38:46.789][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 12:38:46.790][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-12-20 12:38:46.791][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-12-20 12:38:46.792][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-12-20 12:38:46.793][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-12-20 12:38:46.795][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-12-20 12:38:46.796][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-12-20 12:38:46.797][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-12-20 12:38:46.798][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-12-20 12:38:46.799][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-12-20 12:38:46.801][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-12-20 12:38:46.802][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-12-20 12:38:46.803][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-12-20 12:38:46.804][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-12-20 12:38:46.806][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-12-20 12:38:46.807][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-12-20 12:38:46.808][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-12-20 12:38:46.809][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-12-20 12:38:46.810][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-12-20 12:38:46.812][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-12-20 12:38:46.813][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-12-20 12:38:46.814][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-12-20 12:38:46.816][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-12-20 12:38:46.824][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-12-20 12:38:46.825][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-12-20 12:38:46.826][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-12-20 12:38:46.828][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-12-20 12:38:46.829][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-12-20 12:38:46.830][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-12-20 12:38:46.831][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-12-20 12:38:46.832][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-12-20 12:38:46.833][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-12-20 12:38:46.835][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-12-20 12:38:46.836][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-12-20 12:38:46.837][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-12-20 12:38:46.838][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-12-20 12:38:46.839][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-12-20 12:38:46.840][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-12-20 12:38:46.841][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-12-20 12:38:46.843][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-12-20 12:38:46.844][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-12-20 12:38:46.845][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-12-20 12:38:46.846][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-12-20 12:38:46.847][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-12-20 12:38:46.848][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-12-20 12:38:46.849][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-12-20 12:38:46.851][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-12-20 12:38:46.852][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-12-20 12:38:46.853][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 12:38:46.854][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 12:38:46.855][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-12-20 12:38:46.857][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-12-20 12:38:46.858][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-12-20 12:38:46.859][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-12-20 12:38:46.860][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-12-20 12:38:46.861][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-12-20 12:38:46.862][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-12-20 12:38:46.863][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-12-20 12:38:46.864][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-12-20 12:38:46.866][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-12-20 12:38:46.867][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-12-20 12:38:46.868][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-12-20 12:38:46.869][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-12-20 12:38:46.870][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-12-20 12:38:46.871][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-12-20 12:38:46.877][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-12-20 12:38:46.879][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-12-20 12:38:46.883][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:38:46.884][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.885][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.886][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[2024-12-20 12:38:46.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.930][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[2024-12-20 12:38:46.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.935][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.DEBUG[2024-12-20 12:38:46.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.939][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[2024-12-20 12:38:46.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.944][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[2024-12-20 12:38:46.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.949][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[2024-12-20 12:38:46.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.954][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[2024-12-20 12:38:46.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.959][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[2024-12-20 12:38:46.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:46.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.969][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[2024-12-20 12:38:46.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:38:46.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:46.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:46.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:46.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:46.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:46.974][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[2024-12-20 12:38:46.976][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-12-20 12:38:46.991][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-12-20 12:38:46.993][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:46.994][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.995][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.996][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:38:46.997][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:38:46.998][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:46.999][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-12-20 12:38:47.000][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-12-20 12:38:47.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:38:47.002][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:47.002][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-12-20 12:38:47.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-12-20 12:38:47.004][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-12-20 12:38:47.005][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-12-20 12:38:47.006][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:38:47.006][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:38:47.006][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:38:47.007][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-12-20 12:38:47.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:38:47.008][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:38:47.009][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:38:47.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:38:47.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:38:47.011][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:38:47.012][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:47.012][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-12-20 12:38:47.013][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:38:47.014][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:38:47.014][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-12-20 12:38:47.015][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-12-20 12:38:47.015][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-12-20 12:38:47.021][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 12:38:47.023][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 12:38:47.025][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-12-20 12:38:47.026][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 12:38:47.027][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 12:38:47.028][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 12:38:47.059][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-12-20 12:38:47.061][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-12-20 12:38:47.066][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-12-20 12:38:47.071][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-12-20 12:38:47.077][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 12:38:47.078][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 12:38:47.079][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-12-20 12:38:47.080][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-12-20 12:38:47.093][biodb::testThat]
biodb.INFO [2024-12-20 12:38:47.094][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-12-20 12:38:47.095][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:38:47.096][biodb::testThat]
biodb.TRACE[2024-12-20 12:38:47.101][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[2024-12-20 12:38:47.103][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:47.108][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:47.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:47.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:47.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:47.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:47.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:47.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:47.141][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[2024-12-20 12:38:47.153][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.155][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.156][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.174][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:47.175][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:47.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.176][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.203][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:47.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:47.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.207][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:47.208][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:47.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.221][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.223][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:47.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:47.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.227][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:47.228][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:47.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.229][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:47.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:47.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.234][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.235][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.236][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.241][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.242][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.243][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.244][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.248][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:47.248][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.250][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.251][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:47.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.255][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.256][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.258][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.262][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:47.263][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:47.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.265][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:47.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:47.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.269][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:47.270][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.272][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.273][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:47.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.276][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:47.277][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:47.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.280][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.281][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:47.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:47.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:47.350][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-12-20 12:38:47.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:47.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:47.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:47.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:47.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.427][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.441][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 12:38:47.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 12:38:47.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.444][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 12:38:47.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 12:38:47.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.448][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-12-20 12:38:47.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-12-20 12:38:47.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.452][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-12-20 12:38:47.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-12-20 12:38:47.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.564][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.565][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.567][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.591][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.592][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.594][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:47.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:47.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:47.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:47.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:47.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.615][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:47.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:47.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.619][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:47.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:47.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.621][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:47.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:47.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.635][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:47.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:47.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:47.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:47.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.643][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:47.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:47.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.646][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:47.647][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:47.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.649][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:47.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:47.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.673][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.674][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.675][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.702][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.702][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.704][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.717][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:47.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:47.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.721][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:47.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:47.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.731][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:47.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:47.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.734][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:47.735][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:47.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.737][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.737][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:47.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:47.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.749][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.752][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.756][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.759][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.760][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.762][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.762][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.774][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.777][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.781][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.784][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.785][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.786][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.787][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.799][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:47.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:47.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.803][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:47.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:47.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.806][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:47.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:47.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.809][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:47.810][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:47.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.811][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.812][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:47.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:47.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.834][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.834][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.836][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.837][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.848][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:47.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:47.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:47.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:47.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.855][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:47.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:47.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.858][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:47.859][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:47.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.860][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:47.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:47.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.879][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:47.880][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:47.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.882][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.888][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:47.889][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:47.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.890][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.895][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:47.896][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:47.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.898][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.903][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:47.904][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:47.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.905][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.910][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.911][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:47.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.913][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.918][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.919][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:47.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.920][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.925][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.926][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:47.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.928][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.933][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.934][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:47.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.935][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.940][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.941][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:47.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.943][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.948][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:47.949][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:47.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.950][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:47.956][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:47.957][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:47.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:47.958][ef$get] fields variable is a list.
biodb.INFO [2024-12-20 12:38:47.967][biodb::testThat]
biodb.INFO [2024-12-20 12:38:47.968][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-12-20 12:38:47.969][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:38:47.970][biodb::testThat]
biodb.DEBUG[2024-12-20 12:38:47.984][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-12-20 12:38:47.994][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:47.998][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-12-20 12:38:48.000][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:38:48.001][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-12-20 12:38:48.002][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:48.025][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:48.027][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:48.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:48.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:48.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:48.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:48.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:48.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:48.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:48.050][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:48.052][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:48.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.054][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:48.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:48.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.081][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:48.082][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:48.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.084][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.086][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:48.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:48.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.092][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:48.096][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:48.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.098][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.099][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:48.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:48.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.120][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:48.121][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:48.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.123][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:48.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:48.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.128][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:48.129][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:48.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.131][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:48.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:48.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.136][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:48.136][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:48.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.138][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.139][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:48.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:48.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.143][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:48.144][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:48.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.145][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.146][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:48.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:48.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.150][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:48.151][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:48.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.152][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:48.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:48.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.157][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:48.158][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:48.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.159][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:48.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:48.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.164][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:48.165][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:48.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.166][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.167][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:48.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:48.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:48.171][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:48.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.173][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.174][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:48.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:48.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:48.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:48.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:48.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:48.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:48.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:48.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:48.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:48.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:48.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:48.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:48.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:48.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:48.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:48.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:48.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:48.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:48.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:48.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:48.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:48.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:48.217][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-12-20 12:38:48.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-12-20 12:38:48.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-12-20 12:38:48.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-12-20 12:38:48.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-12-20 12:38:48.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-12-20 12:38:48.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-12-20 12:38:48.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 12:38:48.238][biodb::testThat]
biodb.INFO [2024-12-20 12:38:48.239][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-12-20 12:38:48.240][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:38:48.241][biodb::testThat]
biodb.TRACE[2024-12-20 12:38:48.244][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:48.245][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:48.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.247][ef$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:48.249][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-12-20 12:38:48.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:48.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:48.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.283][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:48.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:48.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:48.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:48.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:48.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:48.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:48.294][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-12-20 12:38:48.300][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-12-20 12:38:48.322][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:38:48.338][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-12-20 12:38:48.339][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:38:48.341][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-12-20 12:38:48.372][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[2024-12-20 12:38:48.376][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:48.377][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:48.379][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-12-20 12:38:48.813][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-12-20 12:38:49.085][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:49.088][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-12-20 12:38:49.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-12-20 12:38:49.108][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-12-20 12:38:49.136][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:49.138][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:49.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.139][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.140][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:49.141][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:49.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.143][ef$get] fields variable is a list.
biodb.INFO [2024-12-20 12:38:49.148][biodb::testThat]
biodb.INFO [2024-12-20 12:38:49.149][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-12-20 12:38:49.150][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:38:49.151][biodb::testThat]
biodb.TRACE[2024-12-20 12:38:49.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:49.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:49.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.181][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:49.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:49.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:49.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:49.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:49.250][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:38:49.253][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:38:49.254][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 12:38:49.255][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:38:49.257][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-12-20 12:38:49.273][biodb::testThat]
biodb.INFO [2024-12-20 12:38:49.274][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-12-20 12:38:49.275][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:38:49.275][biodb::testThat]
biodb.TRACE[2024-12-20 12:38:49.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:49.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:49.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:49.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:49.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:49.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:49.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:49.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:49.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:49.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:49.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:49.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.318][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 12:38:49.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 12:38:49.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.321][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 12:38:49.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 12:38:49.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.324][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-12-20 12:38:49.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-12-20 12:38:49.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.328][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-12-20 12:38:49.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-12-20 12:38:49.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:49.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:49.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:49.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:49.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:49.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:49.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:49.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:49.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:49.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:49.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:49.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:49.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.376][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 12:38:49.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 12:38:49.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.379][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-20 12:38:49.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-20 12:38:49.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.383][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-12-20 12:38:49.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-12-20 12:38:49.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:49.386][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-12-20 12:38:49.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-12-20 12:38:49.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:49.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 12:38:49.397][biodb::testThat]
biodb.INFO [2024-12-20 12:38:49.398][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-12-20 12:38:49.399][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:38:49.400][biodb::testThat]
biodb.INFO [2024-12-20 12:38:49.409][biodb::testThat]
biodb.INFO [2024-12-20 12:38:49.410][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-12-20 12:38:49.411][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:38:49.412][biodb::testThat]
biodb.INFO [2024-12-20 12:38:49.421][biodb::testThat]
biodb.INFO [2024-12-20 12:38:49.422][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-12-20 12:38:49.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:38:49.423][biodb::testThat]
biodb.DEBUG[2024-12-20 12:38:49.427][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-12-20 12:38:49.897][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-12-20 12:38:50.606][biodb::testThat]
biodb.INFO [2024-12-20 12:38:50.607][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-12-20 12:38:50.608][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:38:50.609][biodb::testThat]
biodb.DEBUG[2024-12-20 12:38:50.788][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[2024-12-20 12:38:50.904][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:50.905][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:50.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:50.907][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:50.908][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:50.909][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:50.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:50.910][ef$get] fields variable is a list.
biodb.INFO [2024-12-20 12:38:50.913][biodb::testThat]
biodb.INFO [2024-12-20 12:38:50.914][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-12-20 12:38:50.915][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:38:50.915][biodb::testThat]
biodb.TRACE[2024-12-20 12:38:50.928][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:50.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:50.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:50.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:50.932][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:50.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:50.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:50.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:50.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:50.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:50.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:50.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:51.032][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:38:51.036][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:38:51.037][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 12:38:51.038][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:38:51.040][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-12-20 12:38:51.119][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:38:51.123][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:38:51.125][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 12:38:51.126][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:38:51.127][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-12-20 12:38:51.142][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-20 12:38:51.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-20 12:38:51.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.166][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:51.178][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:38:51.204][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:51.205][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:51.221][private$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[2024-12-20 12:38:51.304][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[2024-12-20 12:38:51.396][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:51.398][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-12-20 12:38:51.402][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-12-20 12:38:51.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:51.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:51.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:51.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:51.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:51.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:51.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:51.416][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-12-20 12:38:51.471][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:51.473][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-12-20 12:38:51.475][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:51.476][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:51.477][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:51.478][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:51.479][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:51.479][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:51.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:51.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:51.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:51.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:51.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:51.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:51.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:51.494][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-12-20 12:38:51.497][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:51.498][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:51.499][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-12-20 12:38:51.584][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-12-20 12:38:51.664][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:51.666][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-12-20 12:38:51.670][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-12-20 12:38:51.672][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-12-20 12:38:51.674][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:51.675][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:51.676][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:51.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:51.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:51.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:51.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:51.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:51.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:51.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:51.690][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:51.690][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:51.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.692][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:51.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:51.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.697][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:51.697][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:51.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.699][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.700][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:51.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:51.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.703][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:51.704][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:51.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.706][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.707][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:51.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:51.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.711][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:51.712][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:51.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.713][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:51.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:51.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.718][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:51.719][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:51.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.720][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:51.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:51.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.724][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:51.725][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:51.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.727][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.728][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:51.729][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.730][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.731][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:51.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.735][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:51.736][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:51.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.748][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:51.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:51.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.753][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:51.754][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:51.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.755][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:51.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:51.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.760][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:51.761][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:51.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.762][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.763][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:51.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:51.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.767][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:51.768][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:51.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.769][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.770][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:51.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:51.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:51.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:51.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:51.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:51.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:51.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:51.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:51.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:51.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:51.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:51.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:51.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:51.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:51.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:51.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:51.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:51.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:51.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:51.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:51.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:51.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:51.810][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-12-20 12:38:51.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:51.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:51.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:51.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:51.831][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[2024-12-20 12:38:51.834][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:51.835][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:51.837][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-12-20 12:38:51.926][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-12-20 12:38:52.019][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:52.022][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-12-20 12:38:52.035][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-12-20 12:38:52.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:52.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:52.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:52.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:52.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:52.061][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:52.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:52.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:52.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:52.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:52.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:52.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:52.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:52.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:52.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:52.083][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-12-20 12:38:52.083][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:52.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-12-20 12:38:52.086][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:52.087][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:52.088][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:52.089][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:52.090][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:52.090][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:52.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:52.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:52.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:52.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:52.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:52.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:52.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:52.117][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-12-20 12:38:52.120][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:52.121][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-12-20 12:38:52.122][rule$waitAsNeeded] Wait 0.0986021 second(s).
biodb.TRACE[2024-12-20 12:38:52.223][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-12-20 12:38:52.298][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-12-20 12:38:52.381][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:52.382][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-12-20 12:38:52.384][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-12-20 12:38:52.386][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-12-20 12:38:52.396][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:52.397][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:52.397][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:52.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:52.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:52.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:52.402][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:52.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:52.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:52.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:52.405][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.406][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.407][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.410][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:52.410][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:52.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.412][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.412][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:52.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:52.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.415][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:52.416][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:52.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.417][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.417][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:52.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:52.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.419][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:52.420][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:52.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.420][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:52.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:52.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.422][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:52.423][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:52.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.423][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:52.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:52.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.425][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:52.425][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:52.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.426][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.427][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:52.427][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.428][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.428][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:52.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.430][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:52.430][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:52.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.431][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:52.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:52.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.433][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:52.433][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:52.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.434][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.434][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:52.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:52.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.436][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:52.437][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:52.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.437][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.438][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:52.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:52.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.439][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:52.440][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:52.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.440][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.441][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:52.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:52.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:52.463][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-12-20 12:38:52.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:52.484][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[2024-12-20 12:38:52.486][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:38:52.486][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 12:38:52.487][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:38:52.488][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-12-20 12:38:52.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:52.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:52.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:52.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:52.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:52.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:52.495][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.TRACE[2024-12-20 12:38:52.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:52.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:52.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:52.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:52.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:52.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:52.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:52.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:52.507][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-12-20 12:38:52.507][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:52.513][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-12-20 12:38:52.515][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:52.515][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:52.516][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:52.516][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:52.517][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:52.517][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:52.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:52.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:52.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:52.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:52.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:52.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:52.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:52.524][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-12-20 12:38:52.526][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:52.527][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:52.527][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-12-20 12:38:52.614][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-12-20 12:38:52.691][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:52.693][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-12-20 12:38:52.695][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-12-20 12:38:52.697][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-12-20 12:38:52.698][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:52.698][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:52.699][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:52.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:52.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:52.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:52.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:52.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:52.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:52.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:52.707][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.707][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.708][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.710][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:52.710][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:52.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.711][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.711][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:52.712][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:52.712][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.712][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.713][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:52.713][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:52.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.714][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.715][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:52.715][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:52.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.716][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.716][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:52.716][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:52.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.717][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.718][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:52.718][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.719][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.719][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:52.719][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:52.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.720][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.721][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:52.721][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:52.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.722][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:52.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:52.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.724][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:52.724][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:52.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.725][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.725][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:52.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:52.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.727][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:52.727][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:52.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.733][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:52.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:52.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:52.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:52.755][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-12-20 12:38:52.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:52.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:52.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:52.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:52.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:52.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:52.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:52.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:52.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:52.769][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:52.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:52.770][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-12-20 12:38:52.770][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:52.771][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-12-20 12:38:52.771][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:52.772][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:52.772][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:52.773][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:52.773][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:52.773][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:52.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:52.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:52.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:52.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:52.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:52.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:52.780][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[2024-12-20 12:38:52.781][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-12-20 12:38:52.782][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:52.783][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-12-20 12:38:52.784][rule$waitAsNeeded] Wait 0.0526178 second(s).
biodb.TRACE[2024-12-20 12:38:52.885][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-12-20 12:38:52.957][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-12-20 12:38:53.041][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:53.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-12-20 12:38:53.054][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-12-20 12:38:53.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-12-20 12:38:53.058][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:53.058][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:53.059][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:53.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:53.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:53.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:53.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:53.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:53.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:53.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:53.066][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.067][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.068][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.071][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:53.071][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:53.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.072][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.072][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:53.073][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:53.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.073][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.074][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:53.074][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:53.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.075][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.075][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:53.076][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:53.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.077][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.077][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:53.078][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:53.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.078][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.079][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:53.079][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.080][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.080][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:53.081][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:53.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.081][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.082][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:53.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:53.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.083][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:53.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:53.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.085][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:53.085][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:53.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.086][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.087][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:53.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:53.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.088][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:53.088][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:53.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.089][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:53.128][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-12-20 12:38:53.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:53.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:53.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:53.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:53.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:53.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:53.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:53.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:53.146][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-12-20 12:38:53.146][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:53.147][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-12-20 12:38:53.148][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:53.148][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:53.149][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:53.149][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:53.150][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:53.150][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:53.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:53.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:53.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:53.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:53.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:53.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:53.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:53.157][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-12-20 12:38:53.158][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:53.159][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-12-20 12:38:53.159][rule$waitAsNeeded] Wait 0.0626481 second(s).
biodb.TRACE[2024-12-20 12:38:53.373][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-12-20 12:38:53.452][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-12-20 12:38:53.539][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:53.541][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-12-20 12:38:53.545][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-12-20 12:38:53.547][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-12-20 12:38:53.549][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:53.550][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:53.551][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:53.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:53.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:53.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:53.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:53.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:53.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:53.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:53.566][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.567][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.569][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.576][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:53.577][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:53.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.579][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.581][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:53.593][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:53.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.595][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.597][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:53.598][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:53.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.600][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.601][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:53.602][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:53.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.603][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.605][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:53.605][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:53.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.607][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.608][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:53.609][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.611][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.613][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:53.614][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:53.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.615][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.617][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:53.618][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:53.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.620][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:53.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:53.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.626][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:53.627][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:53.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.628][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.629][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:53.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:53.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.634][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:53.635][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:53.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.636][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:53.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:53.671][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-12-20 12:38:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:53.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:53.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:53.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:53.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:53.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:53.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:53.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:53.710][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-12-20 12:38:53.711][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:53.712][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-12-20 12:38:53.713][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:53.714][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:53.715][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:53.716][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:53.717][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:53.718][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:53.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:53.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:53.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:53.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:53.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:53.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:53.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:53.732][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-12-20 12:38:53.736][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:53.737][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:53.738][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-12-20 12:38:53.822][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-12-20 12:38:53.908][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:53.911][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-12-20 12:38:53.914][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-12-20 12:38:53.917][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-12-20 12:38:53.919][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:53.920][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:53.921][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:53.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:53.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:53.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:53.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:53.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:53.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:53.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:53.936][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.937][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.938][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:53.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:53.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.943][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:53.944][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:53.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.945][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.946][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:53.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:53.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.950][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:53.951][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:53.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.952][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.954][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:53.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:53.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.957][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:53.958][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:53.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.959][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:53.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:53.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.964][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:53.965][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:53.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.966][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:53.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:53.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.971][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:53.972][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:53.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.973][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.974][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:53.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:53.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.987][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:53.989][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.991][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.992][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:53.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:53.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:53.996][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:53.997][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:53.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:53.998][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:54.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:54.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.003][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:54.004][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:54.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.006][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.007][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:54.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:54.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.011][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:54.012][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:54.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.013][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.015][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:54.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:54.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.018][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:54.019][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:54.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.021][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.022][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:54.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:54.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:54.057][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-12-20 12:38:54.058][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:54.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:54.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:54.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:54.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:54.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:54.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:54.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:54.078][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-12-20 12:38:54.079][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:54.081][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-12-20 12:38:54.082][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:54.089][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:54.091][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:54.092][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:54.093][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:54.094][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:54.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:54.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:54.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:54.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:54.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:54.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:54.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:54.107][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-12-20 12:38:54.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:54.111][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:54.113][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-12-20 12:38:54.202][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-12-20 12:38:54.289][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:54.291][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-12-20 12:38:54.295][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-12-20 12:38:54.298][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-12-20 12:38:54.299][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:54.300][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:54.302][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:54.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:54.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:54.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:54.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:54.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:54.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:54.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:54.316][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.317][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.318][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.323][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:54.324][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:54.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.325][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.326][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:54.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:54.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.330][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:54.331][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:54.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.332][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.334][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:54.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:54.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.337][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:54.338][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:54.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.339][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:54.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:54.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.344][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:54.345][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:54.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.346][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:54.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:54.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.351][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:54.352][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:54.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.353][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.355][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:54.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:54.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.358][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:54.359][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.360][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.361][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:54.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.365][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:54.365][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:54.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.373][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:54.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:54.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.382][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:54.383][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:54.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.385][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:54.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:54.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.389][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:54.390][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:54.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.392][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.393][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:54.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:54.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.396][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:54.397][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:54.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.399][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.400][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:54.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:54.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:54.436][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-12-20 12:38:54.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:54.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:54.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:54.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:54.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:54.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:54.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:54.456][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[2024-12-20 12:38:54.457][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-12-20 12:38:54.458][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:54.459][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-12-20 12:38:54.461][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:54.462][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:54.463][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:54.463][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:54.464][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:54.465][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:54.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:54.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:54.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:54.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:54.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:54.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:54.486][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[2024-12-20 12:38:54.487][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-12-20 12:38:54.490][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:54.491][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:54.492][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-12-20 12:38:54.578][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-12-20 12:38:54.662][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:54.665][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-12-20 12:38:54.669][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-12-20 12:38:54.671][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-12-20 12:38:54.673][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:54.674][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:54.676][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:54.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:54.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:54.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:54.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:54.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:54.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:54.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:54.691][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.692][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.693][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.698][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:54.699][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:54.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.701][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.702][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:54.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:54.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.705][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:54.706][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:54.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.708][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.709][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:54.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:54.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.712][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:54.713][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:54.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.714][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:54.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:54.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.719][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:54.720][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:54.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.722][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:54.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:54.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.727][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:54.728][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:54.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.729][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.730][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:54.732][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.734][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.735][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:54.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.738][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:54.739][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:54.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.741][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:54.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:54.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.746][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:54.746][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:54.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.748][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:54.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:54.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.753][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:54.760][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:54.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.769][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.771][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:54.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:54.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.775][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:54.776][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:54.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.778][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.779][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:54.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:54.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:54.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:54.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:54.818][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-12-20 12:38:54.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:54.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:54.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:54.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:54.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:54.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:54.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:54.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:54.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:54.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:54.840][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[2024-12-20 12:38:54.841][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-12-20 12:38:54.842][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:54.844][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-12-20 12:38:54.845][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:54.846][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:54.847][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:54.848][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:54.849][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:54.850][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:54.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:54.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:54.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:54.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:54.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:54.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:54.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:54.863][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-12-20 12:38:54.866][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:54.867][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:54.869][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-12-20 12:38:54.956][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-12-20 12:38:55.048][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:55.051][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-12-20 12:38:55.055][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-12-20 12:38:55.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-12-20 12:38:55.060][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:55.061][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:55.062][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:55.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:55.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:55.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:55.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:55.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:55.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:55.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:55.075][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.077][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.078][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.083][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:55.084][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:55.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.086][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.087][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:55.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:55.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.090][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:55.091][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:55.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.093][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.094][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:55.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:55.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.097][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:55.098][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:55.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.100][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:55.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:55.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.104][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.105][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.107][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.111][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:55.112][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:55.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.113][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.115][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:55.115][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.117][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.118][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:55.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.121][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.122][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.124][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.128][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:55.129][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:55.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.131][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.132][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:55.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:55.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.135][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:55.136][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:55.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.138][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.139][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:55.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:55.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.142][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:55.143][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:55.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.145][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.146][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:55.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:55.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:55.192][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-12-20 12:38:55.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:55.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:55.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:55.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:55.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:55.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:55.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:55.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:55.214][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-12-20 12:38:55.215][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:55.216][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-12-20 12:38:55.218][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:55.219][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:55.220][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:55.220][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:55.221][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:55.222][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:55.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:55.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:55.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:55.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:55.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:55.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:55.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:55.235][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-12-20 12:38:55.238][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:55.239][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:55.241][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-12-20 12:38:55.321][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-12-20 12:38:55.403][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:55.406][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-12-20 12:38:55.410][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-12-20 12:38:55.413][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-12-20 12:38:55.415][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:55.416][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:55.417][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:55.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:55.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:55.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:55.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:55.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:55.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:55.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:55.443][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.444][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.446][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.451][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:55.451][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:55.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.453][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.454][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:55.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:55.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.458][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:55.459][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:55.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.460][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.461][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:55.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:55.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.465][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:55.466][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:55.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.467][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:55.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:55.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.472][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.473][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.474][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.479][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:55.479][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:55.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.481][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.482][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:55.483][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.485][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.486][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:55.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.491][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.492][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.493][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.498][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:55.500][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:55.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.501][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:55.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:55.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.506][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:55.507][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:55.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.509][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.510][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:55.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:55.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.515][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:55.515][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:55.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.518][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.519][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:55.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:55.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:55.568][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-12-20 12:38:55.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:55.580][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:55.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:55.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:55.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:55.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:55.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:55.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:55.590][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-12-20 12:38:55.591][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:55.593][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-12-20 12:38:55.594][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:55.595][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:55.596][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:55.597][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:55.597][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:55.598][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:55.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:55.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:55.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:55.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:55.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:55.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:55.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:55.612][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-12-20 12:38:55.615][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:55.616][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:55.617][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-12-20 12:38:55.705][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-12-20 12:38:55.790][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:55.793][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-12-20 12:38:55.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-12-20 12:38:55.800][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-12-20 12:38:55.802][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:55.803][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:55.804][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:55.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:55.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:55.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:55.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:55.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:55.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:55.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:55.819][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.820][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.822][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.839][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:55.840][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:55.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.842][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.844][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:55.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:55.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.849][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:55.850][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:55.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.851][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.853][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:55.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:55.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.857][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:55.857][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:55.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.859][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:55.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:55.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.864][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.865][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.867][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:55.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.871][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:55.872][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:55.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.873][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.874][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:55.875][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.877][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.878][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:55.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.881][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.882][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.884][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:55.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.888][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:55.889][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:55.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.891][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.892][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:55.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:55.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.895][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:55.896][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:55.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.898][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.899][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:55.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:55.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.902][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:55.903][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:55.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.905][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.906][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:55.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:55.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:55.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:55.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:55.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:55.950][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-12-20 12:38:55.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:55.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:55.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:55.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:55.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:55.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:55.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:55.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:55.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:55.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:55.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:55.973][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-12-20 12:38:55.973][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:55.975][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-12-20 12:38:55.976][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:55.977][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:55.978][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:55.979][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:55.980][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:55.981][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:55.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:55.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:55.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:55.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:55.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:55.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:55.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:55.995][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-12-20 12:38:55.998][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:55.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:56.000][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-12-20 12:38:56.079][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-12-20 12:38:56.157][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:56.160][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-12-20 12:38:56.164][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-12-20 12:38:56.166][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-12-20 12:38:56.168][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:56.169][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:56.170][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:56.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:56.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:56.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:56.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:56.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:56.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:56.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:56.184][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.185][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.187][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.192][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:56.193][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:56.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.194][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.195][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:56.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:56.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.199][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:56.210][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:56.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.212][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:56.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:56.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.217][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:56.218][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:56.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.220][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:56.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:56.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.224][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:56.225][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:56.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.227][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.228][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:56.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:56.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.231][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:56.232][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:56.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.234][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.235][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:56.236][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.237][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.238][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:56.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.242][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.243][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.244][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.249][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:56.249][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:56.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.251][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:56.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:56.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.256][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:56.257][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:56.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.258][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.259][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:56.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:56.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.263][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:56.263][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:56.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.265][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:56.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:56.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:56.310][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-12-20 12:38:56.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:56.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:56.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:56.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:56.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:56.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:56.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:56.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:56.333][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-12-20 12:38:56.334][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:56.335][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-12-20 12:38:56.336][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:56.337][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:56.339][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:56.339][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:56.340][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:56.341][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:56.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:56.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:56.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:56.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:56.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:56.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:56.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:56.355][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-12-20 12:38:56.358][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:56.359][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:56.360][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-12-20 12:38:56.450][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-12-20 12:38:56.546][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:56.549][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-12-20 12:38:56.553][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-12-20 12:38:56.555][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-12-20 12:38:56.557][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:56.558][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:56.559][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:56.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:56.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:56.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:56.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:56.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:56.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:56.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:56.573][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.574][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.576][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.580][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:56.581][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:56.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.583][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.584][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:56.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:56.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.587][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:56.588][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:56.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.590][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:56.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:56.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.594][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:56.595][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:56.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.597][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.604][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:56.609][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:56.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.612][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.613][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:56.614][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:56.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.615][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.617][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:56.618][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.620][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.621][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:56.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.625][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.626][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.628][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.632][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:56.633][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:56.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.635][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.636][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:56.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:56.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.640][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:56.641][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:56.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.643][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.644][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:56.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:56.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.647][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:56.648][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:56.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.650][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:56.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:56.685][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-12-20 12:38:56.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:56.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:56.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:56.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:56.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:56.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:56.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:56.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:56.714][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-12-20 12:38:56.715][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:56.717][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-12-20 12:38:56.718][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:56.719][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:56.720][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:56.721][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:56.722][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:56.723][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:56.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:56.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:56.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:56.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:56.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:56.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:56.735][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.DEBUG[2024-12-20 12:38:56.737][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-12-20 12:38:56.740][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:56.741][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:56.742][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-12-20 12:38:56.826][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-12-20 12:38:56.908][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:56.910][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-12-20 12:38:56.914][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-12-20 12:38:56.917][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-12-20 12:38:56.919][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:56.920][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:56.921][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:56.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:56.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:56.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:56.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:56.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:56.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:56.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:56.935][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.936][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.937][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:56.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:56.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.942][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:56.943][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:56.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.945][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.946][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:56.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:56.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.949][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:56.950][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:56.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.952][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.953][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:56.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:56.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.956][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:56.957][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:56.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.958][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.959][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:56.960][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:56.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.962][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.963][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:56.964][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:56.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.965][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.966][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:56.967][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.969][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.970][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:56.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:56.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.973][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.974][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.976][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:56.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.991][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:56.992][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:56.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.994][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:56.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:56.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:56.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:56.999][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:57.000][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:57.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.001][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.002][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:57.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:57.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.006][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:57.007][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:57.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.008][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:57.042][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-12-20 12:38:57.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:57.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:57.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:57.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:57.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:57.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:57.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:57.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:57.064][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-12-20 12:38:57.065][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:57.066][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-12-20 12:38:57.067][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:57.068][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:57.069][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:57.070][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:57.071][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:57.072][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:57.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:57.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:57.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:57.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:57.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:57.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:57.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:57.092][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-12-20 12:38:57.096][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:57.098][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:57.099][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-12-20 12:38:57.187][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-12-20 12:38:57.275][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:57.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-12-20 12:38:57.282][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-12-20 12:38:57.285][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-12-20 12:38:57.287][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:57.289][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:57.290][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:57.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:57.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:57.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:57.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:57.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:57.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:57.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:57.305][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.306][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.308][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.312][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:57.313][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:57.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.315][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.316][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:57.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:57.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.320][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:57.320][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:57.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.322][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.323][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:57.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:57.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.327][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:57.328][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:57.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.329][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.331][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:57.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:57.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.335][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:57.336][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:57.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.337][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:57.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:57.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.342][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:57.343][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:57.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.344][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.345][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:57.346][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.348][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.349][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:57.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.353][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:57.354][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:57.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.356][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:57.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:57.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.361][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:57.361][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:57.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.363][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:57.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:57.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.368][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:57.369][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:57.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.371][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.372][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:57.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:57.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.389][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:57.390][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:57.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.392][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.394][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:57.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:57.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:57.434][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-12-20 12:38:57.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:57.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:57.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:57.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:57.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:57.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:57.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:57.456][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[2024-12-20 12:38:57.457][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-12-20 12:38:57.458][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:57.460][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-12-20 12:38:57.461][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:57.462][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:57.463][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:57.463][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:57.464][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:57.465][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:57.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:57.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:57.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:57.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:57.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:57.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:57.477][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[2024-12-20 12:38:57.478][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-12-20 12:38:57.481][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:57.482][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:57.484][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-12-20 12:38:57.582][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-12-20 12:38:57.664][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:57.677][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-12-20 12:38:57.687][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-12-20 12:38:57.690][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-12-20 12:38:57.692][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:57.693][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:57.695][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:57.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:57.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:57.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:57.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:57.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:57.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:57.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:57.709][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.710][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.712][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.717][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:57.718][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:57.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.720][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.721][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:57.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:57.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.725][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:57.725][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:57.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.727][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.728][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:57.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:57.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.732][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:57.732][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:57.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.734][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:57.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:57.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.738][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:57.739][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:57.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.741][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:57.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:57.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.746][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:57.747][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:57.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.748][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.749][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:57.750][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.752][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.753][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:57.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.757][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:57.758][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:57.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.759][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:57.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:57.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.764][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:57.765][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:57.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.766][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:57.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:57.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.771][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:57.772][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:57.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.773][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.774][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:57.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:57.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.778][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:57.779][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:57.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.780][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.781][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:57.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:57.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:57.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:57.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:57.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:57.829][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-12-20 12:38:57.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:57.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:57.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:57.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:57.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:57.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:57.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:57.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:57.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:57.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:57.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:57.851][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-12-20 12:38:57.852][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:57.853][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-12-20 12:38:57.854][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:57.855][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:57.856][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:57.857][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:57.858][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:57.859][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:57.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:57.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:57.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:57.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:57.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:57.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:57.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:57.873][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-12-20 12:38:57.876][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:57.876][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:57.878][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-12-20 12:38:57.957][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-12-20 12:38:58.050][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:58.052][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-12-20 12:38:58.056][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-12-20 12:38:58.059][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-12-20 12:38:58.061][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:58.063][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:58.064][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:58.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:58.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:58.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:58.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:58.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:58.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:58.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:58.090][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.091][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.093][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.097][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:58.098][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:58.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.100][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.101][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:58.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:58.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.105][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:58.106][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:58.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.107][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.109][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:58.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:58.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.112][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:58.113][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:58.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.115][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:58.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:58.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.120][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.121][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.122][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.127][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:58.128][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:58.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.129][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.130][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:58.131][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.133][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.134][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:58.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.137][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.138][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.140][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.144][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:58.145][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:58.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.147][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:58.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:58.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.152][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:58.153][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:58.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.154][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.156][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:58.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:58.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.159][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:58.160][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:58.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.161][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.162][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:58.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:58.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:58.213][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-12-20 12:38:58.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:58.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:58.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:58.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:58.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:58.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:58.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:58.237][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[2024-12-20 12:38:58.238][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-12-20 12:38:58.239][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:58.241][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-12-20 12:38:58.242][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:58.243][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:58.244][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:58.245][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:58.246][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:58.247][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:58.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:58.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:58.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:58.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:58.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:58.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:58.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:58.261][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-12-20 12:38:58.264][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:58.265][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:58.266][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-12-20 12:38:58.367][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-12-20 12:38:58.456][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:58.458][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-12-20 12:38:58.463][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-12-20 12:38:58.465][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-12-20 12:38:58.467][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:58.468][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:58.469][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:58.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:58.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:58.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:58.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:58.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:58.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:58.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:58.483][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.485][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.486][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.502][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:58.503][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:58.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.505][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.506][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:58.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:58.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.510][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:58.511][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:58.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.512][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.513][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:58.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:58.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.517][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:58.517][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:58.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.519][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.520][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:58.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:58.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.524][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.525][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.526][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.531][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:58.532][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:58.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.533][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.534][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:58.535][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.537][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.538][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:58.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.541][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.542][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.543][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.548][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:58.549][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:58.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.550][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:58.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:58.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.555][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:58.555][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:58.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.557][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.558][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:58.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:58.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.561][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:58.562][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:58.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.564][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.565][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:58.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:58.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:58.608][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-12-20 12:38:58.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:58.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:58.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:58.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:58.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:58.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:58.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:58.629][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[2024-12-20 12:38:58.630][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-12-20 12:38:58.631][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:58.632][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-12-20 12:38:58.633][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:58.634][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:58.635][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:58.636][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:58.637][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:58.638][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:58.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:58.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:58.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:58.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:58.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:58.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:58.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:58.651][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-12-20 12:38:58.654][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:58.655][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:58.656][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-12-20 12:38:58.734][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-12-20 12:38:58.819][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:58.822][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-12-20 12:38:58.826][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-12-20 12:38:58.829][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-12-20 12:38:58.831][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:58.832][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:58.833][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:58.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:58.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:58.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:58.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:58.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:58.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:58.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:58.848][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.849][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.850][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.855][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:58.856][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:58.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.857][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.859][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:58.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:58.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.862][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:58.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:58.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.876][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.877][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:58.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:58.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.882][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:58.883][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:58.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.884][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:58.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:58.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.889][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.890][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.891][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:58.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.896][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:58.897][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:58.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.898][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.899][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:58.900][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.902][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.903][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:58.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.906][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.907][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.909][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:58.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.913][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:58.914][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:58.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.916][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:58.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:58.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.920][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:58.921][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:58.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.923][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.924][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:58.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:58.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.927][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:58.928][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:58.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.930][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.931][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:58.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:58.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:58.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:58.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:58.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:58.975][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-12-20 12:38:58.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:58.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:58.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:58.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:58.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:58.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:58.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:58.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:58.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:58.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:58.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:58.999][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-12-20 12:38:59.000][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:59.002][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-12-20 12:38:59.003][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:59.004][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:59.005][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:59.006][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:59.007][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:59.008][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:59.010][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.020][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[2024-12-20 12:38:59.022][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-12-20 12:38:59.025][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:59.026][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:59.027][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-12-20 12:38:59.115][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-12-20 12:38:59.194][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:59.197][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-12-20 12:38:59.200][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-12-20 12:38:59.203][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-12-20 12:38:59.205][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:59.207][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:59.208][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:59.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:59.222][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.223][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.225][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.229][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:59.230][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:59.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.232][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.233][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:59.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:59.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.236][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:59.237][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:59.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.239][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.240][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:59.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:59.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.243][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:59.244][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:59.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.246][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:59.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:59.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.264][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:59.265][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:59.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.268][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:59.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:59.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.273][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:59.274][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:59.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.275][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.277][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:59.278][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.279][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.280][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:59.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.284][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:59.285][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:59.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.286][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:59.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:59.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.291][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:59.292][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:59.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.294][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:59.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:59.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.298][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:59.299][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:59.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.301][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.302][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:59.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:59.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.305][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:59.306][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:59.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.308][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.309][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:59.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:59.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.347][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-12-20 12:38:59.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:59.378][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-12-20 12:38:59.379][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:38:59.381][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-12-20 12:38:59.382][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:38:59.383][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:38:59.384][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:38:59.385][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:38:59.386][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:38:59.386][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:38:59.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:38:59.400][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-12-20 12:38:59.403][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:38:59.404][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:38:59.405][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-12-20 12:38:59.492][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-12-20 12:38:59.581][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:38:59.583][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-12-20 12:38:59.587][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-12-20 12:38:59.590][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-12-20 12:38:59.591][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:38:59.592][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:38:59.593][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:38:59.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:59.607][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.609][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.614][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:59.615][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:59.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.617][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.618][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:38:59.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:38:59.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.621][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:59.622][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:59.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.623][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.625][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:38:59.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:38:59.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.628][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:59.629][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:59.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.630][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:38:59.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:38:59.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.635][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:59.636][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:59.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.637][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.638][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:38:59.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:38:59.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.652][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:59.654][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:38:59.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.656][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.658][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:59.659][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.660][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.661][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:38:59.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.665][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:59.665][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:59.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.667][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:59.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:38:59.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.671][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:59.672][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:59.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.674][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.675][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:38:59.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:38:59.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.679][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:59.680][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:59.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.681][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.682][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:38:59.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:38:59.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.686][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:59.686][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:59.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.688][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.689][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:38:59.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:38:59.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:38:59.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:38:59.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:38:59.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.728][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-12-20 12:38:59.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.768][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[2024-12-20 12:38:59.772][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:38:59.773][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 12:38:59.774][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:38:59.776][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-12-20 12:38:59.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:59.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:59.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:59.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:59.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:59.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:59.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:38:59.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.969][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.TRACE[2024-12-20 12:38:59.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:38:59.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:38:59.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:38:59.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:38:59.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:38:59.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:38:59.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:38:59.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:38:59.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:38:59.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:38:59.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:00.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:00.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:00.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.066][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.TRACE[2024-12-20 12:39:00.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.088][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.TRACE[2024-12-20 12:39:00.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:00.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.141][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[2024-12-20 12:39:00.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:00.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.182][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:00.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:00.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:00.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:00.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:00.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:00.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:00.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:00.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:00.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:00.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:00.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:00.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:00.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:00.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:00.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:00.337][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[2024-12-20 12:39:00.341][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:00.342][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:00.344][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-12-20 12:39:00.425][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-12-20 12:39:00.519][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:00.522][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-12-20 12:39:00.526][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-12-20 12:39:00.530][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:00.534][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:00.535][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:00.537][private$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[2024-12-20 12:39:00.627][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[2024-12-20 12:39:00.716][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:00.718][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-12-20 12:39:00.723][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-12-20 12:39:00.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:00.738][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-12-20 12:39:00.738][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:39:00.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-12-20 12:39:00.741][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:39:00.742][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:39:00.743][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:39:00.744][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:39:00.745][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:39:00.746][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:39:00.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:00.759][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-12-20 12:39:00.762][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:00.763][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:00.764][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-12-20 12:39:00.844][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-12-20 12:39:00.934][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:00.936][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-12-20 12:39:00.940][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-12-20 12:39:00.943][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-12-20 12:39:00.945][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:39:00.946][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:39:00.947][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:39:00.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:00.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:00.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:00.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:00.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:00.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:00.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:00.979][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:00.980][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:00.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.981][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:00.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:00.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.986][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:00.987][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:00.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.988][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.989][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:00.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:00.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.993][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:00.994][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:00.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.995][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:00.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:00.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:00.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:00.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.000][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:01.001][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:01.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.003][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:01.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:01.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.007][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:01.008][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:01.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.010][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:01.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:01.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.014][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:01.015][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:01.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.016][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.017][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:01.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:01.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.021][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:01.022][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:01.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.023][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.024][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:01.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:01.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.028][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.028][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.030][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.034][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:01.035][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:01.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.037][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:01.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:01.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.041][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:01.042][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:01.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.044][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.045][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:01.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:01.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.048][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:01.049][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:01.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.051][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.052][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:01.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:01.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:01.099][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-12-20 12:39:01.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:01.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:01.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:01.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:01.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:01.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:01.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:01.122][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[2024-12-20 12:39:01.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:01.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:01.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:01.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:01.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:01.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:01.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:01.142][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[2024-12-20 12:39:01.143][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-12-20 12:39:01.144][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:39:01.146][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-12-20 12:39:01.147][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:39:01.148][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:39:01.149][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:39:01.150][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:39:01.150][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:39:01.151][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:39:01.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:01.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:01.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:01.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:01.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:01.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:01.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:01.164][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-12-20 12:39:01.167][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:01.168][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-12-20 12:39:01.176][rule$waitAsNeeded] Wait 0.167119 second(s).
biodb.TRACE[2024-12-20 12:39:01.496][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-12-20 12:39:01.591][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-12-20 12:39:01.684][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:01.687][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-12-20 12:39:01.691][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-12-20 12:39:01.693][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-12-20 12:39:01.695][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:39:01.696][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:39:01.697][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:39:01.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:01.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:01.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:01.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:01.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:01.707][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:01.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:01.711][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.712][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.714][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.718][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:01.719][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:01.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.721][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.722][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:01.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:01.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.725][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:01.726][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:01.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.728][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:01.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:01.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.732][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:01.733][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:01.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.735][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:01.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:01.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.739][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:01.740][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:01.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.741][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:01.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:01.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.746][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:01.747][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:01.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.749][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.750][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:01.751][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:01.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.752][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.754][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:01.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:01.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.757][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.758][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.761][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.765][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:01.766][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:01.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.768][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:01.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:01.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.772][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:01.773][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:01.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.775][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.776][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:01.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:01.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.789][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:01.790][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:01.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.793][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.794][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:01.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:01.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:01.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:01.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:01.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:01.835][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-12-20 12:39:01.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:01.866][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:01.871][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:01.872][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 12:39:01.874][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:01.875][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-12-20 12:39:01.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:01.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:01.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:01.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:01.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:01.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:01.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:01.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:01.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:01.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:01.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.578][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:02.582][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:02.584][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-12-20 12:39:02.586][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:02.588][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-12-20 12:39:02.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:02.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:02.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:02.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:02.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:02.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:02.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:02.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:02.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:02.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:02.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:02.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:03.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:03.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.065][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-12-20 12:39:03.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-12-20 12:39:03.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 12:39:03.078][biodb::testThat]
biodb.INFO [2024-12-20 12:39:03.079][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-12-20 12:39:03.081][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:03.082][biodb::testThat]
biodb.TRACE[2024-12-20 12:39:03.087][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-20 12:39:03.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-20 12:39:03.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:03.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:03.125][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:03.128][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:03.130][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-12-20 12:39:03.131][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:03.133][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-12-20 12:39:03.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:03.166][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:03.170][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:03.171][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-12-20 12:39:03.172][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:03.173][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-12-20 12:39:03.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:03.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:03.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:03.219][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 12:39:03.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.238][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.238][private$selectFields]
biodb.TRACE[2024-12-20 12:39:03.239][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:03.240][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:03.241][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.242][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.243][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.244][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.245][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.246][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.248][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.248][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.249][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.250][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.251][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.252][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.253][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:03.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.273][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-12-20 12:39:03.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.292][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.293][private$selectFields]
biodb.TRACE[2024-12-20 12:39:03.294][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:03.295][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:03.296][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.296][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.297][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.299][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.300][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.302][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.303][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.304][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.306][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.307][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.308][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:03.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.322][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 12:39:03.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.341][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.341][private$selectFields]
biodb.TRACE[2024-12-20 12:39:03.342][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:03.343][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:03.344][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.345][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.346][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.347][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.348][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.349][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.350][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.351][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.352][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.353][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.354][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.355][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.356][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:03.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.367][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-12-20 12:39:03.368][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 12:39:03.369][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 12:39:03.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:03.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.448][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:03.460][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:03.463][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:03.464][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:03.466][private$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[2024-12-20 12:39:03.550][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[2024-12-20 12:39:03.631][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:03.641][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-12-20 12:39:03.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-12-20 12:39:03.653][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[2024-12-20 12:39:03.657][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:03.658][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:03.659][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-12-20 12:39:03.757][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-12-20 12:39:03.837][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:03.839][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-12-20 12:39:03.843][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-12-20 12:39:03.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.856][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:03.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:03.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:03.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:03.933][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 12:39:03.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:03.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:03.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:03.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:03.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:03.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:03.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:03.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.975][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.976][private$selectFields]
biodb.TRACE[2024-12-20 12:39:03.976][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:03.977][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:03.978][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.979][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.980][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.982][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.983][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.983][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.985][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.986][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.987][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:03.988][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.989][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.990][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.991][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:03.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:03.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:03.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:03.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.002][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-12-20 12:39:04.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.053][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.054][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.055][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.056][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.057][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.057][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.058][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.060][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.061][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.062][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.063][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.064][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.074][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.075][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.076][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.078][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.078][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.089][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 12:39:04.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.109][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.109][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.110][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.111][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.112][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.113][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.114][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.115][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.116][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.116][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.117][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.125][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.126][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.126][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.126][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.127][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.127][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.132][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-12-20 12:39:04.132][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 12:39:04.132][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 12:39:04.137][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-12-20 12:39:04.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-12-20 12:39:04.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 12:39:04.141][biodb::testThat]
biodb.INFO [2024-12-20 12:39:04.142][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-12-20 12:39:04.142][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:04.142][biodb::testThat]
biodb.TRACE[2024-12-20 12:39:04.144][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-20 12:39:04.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-20 12:39:04.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:04.160][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:04.162][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:04.164][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-12-20 12:39:04.165][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:04.166][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-12-20 12:39:04.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.180][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:04.182][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:04.183][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-12-20 12:39:04.183][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:04.184][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-12-20 12:39:04.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.186][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.211][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 12:39:04.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.221][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.221][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.222][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.222][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.223][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.224][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.225][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.227][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.228][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.229][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.231][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.231][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.232][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.236][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.236][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.247][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-12-20 12:39:04.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.267][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.268][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.268][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.269][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.270][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.271][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.272][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.273][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.274][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.275][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.276][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.277][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.278][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.278][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.279][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.281][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.281][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.292][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 12:39:04.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.311][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.311][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.312][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.312][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.313][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.313][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.313][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.314][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.314][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.315][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.315][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.316][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.316][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.316][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.317][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.317][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.318][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.329][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-12-20 12:39:04.330][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 12:39:04.330][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 12:39:04.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:04.371][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:04.375][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:04.376][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-12-20 12:39:04.377][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:04.379][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-12-20 12:39:04.382][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:04.385][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:04.386][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-12-20 12:39:04.388][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:04.389][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-12-20 12:39:04.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.454][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 12:39:04.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.473][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.473][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.474][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.475][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.476][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.477][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.478][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.479][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.480][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.481][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.483][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.483][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.484][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.485][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.486][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.487][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.488][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.499][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-12-20 12:39:04.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.518][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.518][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.519][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.520][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.521][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.521][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.522][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.524][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.525][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.526][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.527][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.528][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.529][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.530][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.530][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.532][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.533][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.544][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 12:39:04.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.561][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.562][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.563][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.564][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.564][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.565][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.566][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.568][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.568][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.569][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.571][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.571][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.572][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.573][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.574][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.575][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.576][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.587][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-12-20 12:39:04.588][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 12:39:04.589][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 12:39:04.598][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-12-20 12:39:04.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-12-20 12:39:04.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 12:39:04.606][biodb::testThat]
biodb.INFO [2024-12-20 12:39:04.607][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-12-20 12:39:04.608][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:04.608][biodb::testThat]
biodb.TRACE[2024-12-20 12:39:04.612][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-20 12:39:04.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-20 12:39:04.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:04.648][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:04.651][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:04.653][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-12-20 12:39:04.654][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:04.655][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-12-20 12:39:04.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.681][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:04.684][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:04.684][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-12-20 12:39:04.685][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:04.686][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-12-20 12:39:04.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:04.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.711][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 12:39:04.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.725][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.725][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.725][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.725][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.726][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.726][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.727][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.727][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.727][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.728][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.729][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.729][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.729][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.730][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.730][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.731][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.731][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.736][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-12-20 12:39:04.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.747][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.747][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.748][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.748][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.749][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.750][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.750][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.751][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.751][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.752][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.753][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.753][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.753][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.754][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.754][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.755][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.755][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.760][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 12:39:04.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.770][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.770][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.771][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.771][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.771][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.772][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.772][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.772][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.773][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.773][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.774][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.774][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.775][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.775][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.776][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.776][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.777][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.784][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-12-20 12:39:04.784][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 12:39:04.785][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 12:39:04.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:04.818][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:04.821][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:04.822][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-12-20 12:39:04.823][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:04.824][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-12-20 12:39:04.826][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:04.828][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:04.829][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-12-20 12:39:04.829][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:04.830][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-12-20 12:39:04.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.865][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:04.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:04.879][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-12-20 12:39:04.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.898][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.899][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.900][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.901][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.901][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.902][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.903][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.905][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.905][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.906][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.908][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.909][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.910][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.911][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.913][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.913][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.920][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-12-20 12:39:04.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.929][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.929][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.929][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.930][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.930][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.931][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.931][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.932][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.932][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.932][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.933][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.933][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.934][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.934][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.935][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.935][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.936][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.941][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-12-20 12:39:04.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:04.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:04.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:04.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:04.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:04.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:04.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:04.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.951][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.951][private$selectFields]
biodb.TRACE[2024-12-20 12:39:04.951][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-12-20 12:39:04.952][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-12-20 12:39:04.952][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.953][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.953][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.953][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.954][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.954][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.955][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.955][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.956][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-12-20 12:39:04.956][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.956][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.957][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.957][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-12-20 12:39:04.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:04.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:04.964][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-12-20 12:39:04.965][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-12-20 12:39:04.966][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-12-20 12:39:04.982][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-12-20 12:39:04.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-12-20 12:39:04.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:04.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-20 12:39:04.991][biodb::testThat]
biodb.INFO [2024-12-20 12:39:04.992][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-12-20 12:39:04.993][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:04.993][biodb::testThat]
biodb.DEBUG[2024-12-20 12:39:04.994][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-12-20 12:39:04.994][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:39:04.995][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-12-20 12:39:04.996][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:39:04.996][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:39:04.997][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:39:04.997][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:39:04.998][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:39:04.998][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:39:05.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:05.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:05.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:05.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:05.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:05.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:05.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:05.008][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-12-20 12:39:05.010][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:05.010][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:05.011][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-12-20 12:39:05.098][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-12-20 12:39:05.178][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:05.181][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-12-20 12:39:05.184][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-12-20 12:39:05.187][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-12-20 12:39:05.189][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:39:05.190][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:39:05.191][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:39:05.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:05.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:05.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:05.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:05.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:05.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:05.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:05.205][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.206][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.207][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.212][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:05.213][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:05.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.214][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.216][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:05.217][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:05.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.218][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.219][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:05.220][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:05.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.222][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.223][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.224][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.225][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.226][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.227][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.229][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.230][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:05.231][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:05.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.232][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.233][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:05.234][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:05.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.236][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.237][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:05.237][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:05.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.239][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.240][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:05.241][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:05.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.243][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.244][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:05.245][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:05.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.246][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:05.283][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-12-20 12:39:05.284][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-12-20 12:39:05.302][biodb::testThat]
biodb.INFO [2024-12-20 12:39:05.303][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-12-20 12:39:05.304][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:05.304][biodb::testThat]
biodb.DEBUG[2024-12-20 12:39:05.315][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-12-20 12:39:05.316][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-12-20 12:39:05.317][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-12-20 12:39:05.319][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-12-20 12:39:05.320][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2024-12-20 12:39:05.322][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2024-12-20 12:39:05.323][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:39:05.324][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:39:05.325][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:39:05.326][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:39:05.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:05.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:05.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:05.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:05.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:05.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:05.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:05.341][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-12-20 12:39:05.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:05.344][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:05.346][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-12-20 12:39:05.429][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-12-20 12:39:05.522][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:05.524][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-12-20 12:39:05.528][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-12-20 12:39:05.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:05.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:05.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:05.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:05.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:05.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:05.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:05.542][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-12-20 12:39:05.545][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:05.546][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:05.547][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-12-20 12:39:05.635][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-12-20 12:39:05.716][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:05.718][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-12-20 12:39:05.722][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-12-20 12:39:05.725][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-12-20 12:39:05.727][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:39:05.728][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-12-20 12:39:05.729][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-12-20 12:39:05.731][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:05.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:05.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:05.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:05.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:05.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:05.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:05.743][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.744][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.746][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.750][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:05.751][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:05.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.753][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.754][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:05.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:05.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.756][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.758][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:05.759][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:05.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.760][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.761][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.762][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.764][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.765][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.765][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.767][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.768][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:05.769][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:05.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.771][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.772][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:05.773][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:05.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.774][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.775][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:05.776][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:05.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.778][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.779][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:05.780][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:05.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.781][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.783][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:05.784][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:05.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.785][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:05.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:05.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:05.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:05.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:05.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:05.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:05.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:05.821][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.822][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.823][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.828][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:05.828][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:05.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.830][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.831][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:05.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:05.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.834][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:05.835][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:05.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.837][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.838][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:05.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:05.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.841][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:05.842][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:05.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.844][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:05.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:05.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.848][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.849][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.850][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.855][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.856][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.857][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.860][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.865][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:05.866][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:05.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.868][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.869][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:05.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:05.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.873][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:05.873][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:05.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.875][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:05.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:05.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.880][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:05.881][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:05.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.883][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:05.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:05.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.888][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:05.889][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:05.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.890][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.891][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:05.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:05.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.895][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:05.896][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:05.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.897][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.898][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:05.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:05.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:05.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:05.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:05.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:05.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:05.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:05.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:05.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:05.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:05.937][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.938][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.939][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:05.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:05.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.944][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:05.945][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:05.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.947][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.948][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:05.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:05.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.951][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:05.952][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:05.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.954][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.955][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:05.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:05.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.959][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:05.960][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:05.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.973][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.975][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:05.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:05.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.978][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.979][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.981][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:05.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.985][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.986][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.987][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.988][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:05.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.992][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:05.993][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:05.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.994][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.996][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:05.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:05.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:05.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:05.999][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:06.000][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:06.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.002][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:06.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:06.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.007][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:06.008][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:06.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.010][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:06.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:06.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.014][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:06.015][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:06.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.017][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.018][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:06.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:06.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.021][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:06.022][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:06.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.023][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.024][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:06.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:06.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:06.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:06.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:06.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:06.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:06.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:06.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:06.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:06.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:06.081][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-12-20 12:39:06.082][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-12-20 12:39:06.082][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-12-20 12:39:06.097][biodb::testThat]
biodb.INFO [2024-12-20 12:39:06.098][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-12-20 12:39:06.099][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:06.100][biodb::testThat]
biodb.INFO [2024-12-20 12:39:06.126][biodb::testThat]
biodb.INFO [2024-12-20 12:39:06.128][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-12-20 12:39:06.129][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:06.129][biodb::testThat]
biodb.INFO [2024-12-20 12:39:06.138][biodb::testThat]
biodb.INFO [2024-12-20 12:39:06.139][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-12-20 12:39:06.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:06.141][biodb::testThat]
biodb.DEBUG[2024-12-20 12:39:06.143][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[2024-12-20 12:39:06.147][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:06.148][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:06.150][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-12-20 12:39:06.354][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-12-20 12:39:06.534][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:06.536][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-12-20 12:39:06.541][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-12-20 12:39:06.553][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:06.554][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:06.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.556][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:06.557][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:06.558][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:06.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:06.559][ef$get] fields variable is a list.
biodb.INFO [2024-12-20 12:39:06.561][biodb::testThat]
biodb.INFO [2024-12-20 12:39:06.562][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-12-20 12:39:06.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:06.564][biodb::testThat]
biodb.ERROR[2024-12-20 12:39:06.578][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-12-20 12:39:06.596][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-12-20 12:39:06.610][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-12-20 12:39:06.612][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-12-20 12:39:06.613][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-12-20 12:39:06.614][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-12-20 12:39:06.614][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:06.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:06.616][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.617][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-12-20 12:39:06.629][biodb::testContext]
biodb.INFO [2024-12-20 12:39:06.630][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 12:39:06.631][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-12-20 12:39:06.631][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 12:39:06.632][biodb::testContext]
biodb.INFO [2024-12-20 12:39:06.635][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-12-20 12:39:06.637][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-12-20 12:39:06.642][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:39:06.643][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-12-20 12:39:06.644][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-12-20 12:39:06.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.646][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[2024-12-20 12:39:06.647][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-12-20 12:39:06.649][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-12-20 12:39:06.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.652][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-12-20 12:39:06.653][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-12-20 12:39:06.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.655][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[2024-12-20 12:39:06.656][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-12-20 12:39:06.657][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-12-20 12:39:06.658][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-12-20 12:39:06.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.661][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-12-20 12:39:06.662][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-12-20 12:39:06.662][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-12-20 12:39:06.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.666][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[2024-12-20 12:39:06.667][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-12-20 12:39:06.668][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-12-20 12:39:06.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.671][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-12-20 12:39:06.672][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-12-20 12:39:06.673][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-12-20 12:39:06.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.676][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-12-20 12:39:06.677][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-12-20 12:39:06.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.680][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-12-20 12:39:06.692][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-12-20 12:39:06.693][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-12-20 12:39:06.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.696][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[2024-12-20 12:39:06.697][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-12-20 12:39:06.697][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-12-20 12:39:06.698][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-12-20 12:39:06.699][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-12-20 12:39:06.700][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-12-20 12:39:06.701][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-12-20 12:39:06.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.703][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-12-20 12:39:06.704][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-12-20 12:39:06.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.706][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[2024-12-20 12:39:06.707][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-12-20 12:39:06.708][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-12-20 12:39:06.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.711][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-12-20 12:39:06.712][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-12-20 12:39:06.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.715][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-12-20 12:39:06.715][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-12-20 12:39:06.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.718][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-12-20 12:39:06.719][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-12-20 12:39:06.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.722][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-12-20 12:39:06.723][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-12-20 12:39:06.740][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-12-20 12:39:06.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.744][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-12-20 12:39:06.745][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-12-20 12:39:06.746][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-12-20 12:39:06.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.750][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-12-20 12:39:06.752][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.753][self$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[2024-12-20 12:39:06.753][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.754][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:06.755][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.756][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.757][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.758][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.758][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 12:39:06.759][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:06.760][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.761][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-12-20 12:39:06.762][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:06.762][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.763][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.764][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:39:06.764][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:39:06.764][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:39:06.764][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 12:39:06.764][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 12:39:06.765][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:06.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:06.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:06.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:06.768][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:06.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:06.770][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.771][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:06.772][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:06.773][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.774][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.775][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-12-20 12:39:06.777][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.778][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 12:39:06.779][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.780][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:06.781][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.782][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.783][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.784][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.785][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 12:39:06.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:06.786][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.787][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-12-20 12:39:06.788][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:06.789][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.790][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.791][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:39:06.791][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:39:06.791][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:39:06.791][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 12:39:06.791][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 12:39:06.792][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:06.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:06.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:06.794][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:06.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:06.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:06.797][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.798][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.798][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:06.799][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:06.800][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.801][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.802][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-12-20 12:39:06.804][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.805][self$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[2024-12-20 12:39:06.806][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.807][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:06.808][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.809][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.810][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.811][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.812][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 12:39:06.812][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:06.813][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.814][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-12-20 12:39:06.815][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:06.816][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.817][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.818][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.819][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:06.819][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:06.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:06.821][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:06.822][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:06.823][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:06.823][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.824][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.825][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:06.826][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:06.827][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.828][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.830][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-12-20 12:39:06.832][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.833][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 12:39:06.834][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.835][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:06.836][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.837][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.838][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.838][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.839][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 12:39:06.840][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:06.841][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.842][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-12-20 12:39:06.843][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:06.843][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.844][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:06.845][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.846][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:06.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:06.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:06.848][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:06.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:06.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:06.850][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:06.851][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.852][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:06.853][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:06.853][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:06.854][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:06.855][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:39:06.856][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.857][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[2024-12-20 12:39:06.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.864][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[2024-12-20 12:39:06.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.903][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.DEBUG[2024-12-20 12:39:06.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:06.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:06.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:06.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:06.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:06.922][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-12-20 12:39:06.923][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-12-20 12:39:06.924][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-12-20 12:39:06.925][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-12-20 12:39:06.927][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 12:39:06.928][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-12-20 12:39:06.929][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-12-20 12:39:06.930][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-12-20 12:39:06.931][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-12-20 12:39:06.933][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-12-20 12:39:06.934][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 12:39:06.935][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-12-20 12:39:06.936][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-12-20 12:39:06.938][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-12-20 12:39:06.939][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-12-20 12:39:06.940][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-12-20 12:39:06.941][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-12-20 12:39:06.943][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-12-20 12:39:06.944][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 12:39:06.945][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-12-20 12:39:06.946][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-12-20 12:39:06.948][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-12-20 12:39:06.949][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-12-20 12:39:06.950][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-12-20 12:39:06.951][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-12-20 12:39:06.952][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-12-20 12:39:06.954][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-12-20 12:39:06.955][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-12-20 12:39:06.956][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-12-20 12:39:06.957][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-12-20 12:39:06.959][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-12-20 12:39:06.960][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-12-20 12:39:06.961][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-12-20 12:39:06.962][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-12-20 12:39:06.963][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-12-20 12:39:06.965][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-12-20 12:39:06.966][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-12-20 12:39:06.967][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-12-20 12:39:06.968][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-12-20 12:39:06.970][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-12-20 12:39:06.971][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-12-20 12:39:06.972][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-12-20 12:39:06.973][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-12-20 12:39:06.974][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-12-20 12:39:06.976][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-12-20 12:39:06.977][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-12-20 12:39:06.978][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-12-20 12:39:06.979][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-12-20 12:39:06.981][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-12-20 12:39:06.982][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-12-20 12:39:06.983][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-12-20 12:39:06.985][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-12-20 12:39:06.986][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-12-20 12:39:06.987][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-12-20 12:39:06.988][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-12-20 12:39:06.989][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-12-20 12:39:06.991][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-12-20 12:39:06.992][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-12-20 12:39:07.000][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-12-20 12:39:07.002][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-12-20 12:39:07.003][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-12-20 12:39:07.004][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-12-20 12:39:07.005][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-12-20 12:39:07.006][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-12-20 12:39:07.008][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-12-20 12:39:07.009][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-12-20 12:39:07.010][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 12:39:07.011][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 12:39:07.012][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-12-20 12:39:07.013][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-12-20 12:39:07.014][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-12-20 12:39:07.016][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-12-20 12:39:07.017][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-12-20 12:39:07.018][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-12-20 12:39:07.019][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-12-20 12:39:07.020][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-12-20 12:39:07.021][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-12-20 12:39:07.022][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-12-20 12:39:07.024][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-12-20 12:39:07.025][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-12-20 12:39:07.026][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-12-20 12:39:07.027][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-12-20 12:39:07.028][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-12-20 12:39:07.029][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-12-20 12:39:07.031][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-12-20 12:39:07.032][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:39:07.033][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.034][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.035][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[2024-12-20 12:39:07.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.040][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[2024-12-20 12:39:07.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.046][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[2024-12-20 12:39:07.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.064][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[2024-12-20 12:39:07.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.072][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[2024-12-20 12:39:07.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.104][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[2024-12-20 12:39:07.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.122][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[2024-12-20 12:39:07.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.140][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-12-20 12:39:07.141][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-12-20 12:39:07.143][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:07.144][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-12-20 12:39:07.145][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.146][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:07.147][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.148][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:07.149][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.149][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-12-20 12:39:07.150][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-12-20 12:39:07.151][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:07.152][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.153][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-12-20 12:39:07.154][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-12-20 12:39:07.156][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:07.156][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:39:07.156][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:39:07.156][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:39:07.157][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-12-20 12:39:07.158][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:07.159][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:07.160][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:07.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:07.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:07.162][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:07.163][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:39:07.163][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-12-20 12:39:07.164][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:07.164][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:07.165][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.166][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-12-20 12:39:07.166][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-12-20 12:39:07.167][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 12:39:07.169][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 12:39:07.170][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-12-20 12:39:07.172][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 12:39:07.173][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 12:39:07.175][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 12:39:07.178][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-12-20 12:39:07.179][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-12-20 12:39:07.180][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-12-20 12:39:07.182][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-12-20 12:39:07.183][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 12:39:07.184][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 12:39:07.185][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-12-20 12:39:07.186][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-12-20 12:39:07.187][biodb::testThat]
biodb.INFO [2024-12-20 12:39:07.188][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-12-20 12:39:07.189][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:07.190][biodb::testThat]
biodb.DEBUG[2024-12-20 12:39:07.194][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-12-20 12:39:07.198][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:07.199][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-12-20 12:39:07.200][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:07.202][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-12-20 12:39:07.205][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:07.211][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:07.212][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-12-20 12:39:07.214][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:07.216][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-12-20 12:39:07.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.246][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:07.250][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:07.252][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-12-20 12:39:07.253][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:07.255][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-12-20 12:39:07.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.267][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.DEBUG[2024-12-20 12:39:07.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.299][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:07.302][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:07.304][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-12-20 12:39:07.305][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:07.306][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-12-20 12:39:07.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.319][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:07.323][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:07.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-12-20 12:39:07.333][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:07.334][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-12-20 12:39:07.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.360][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:07.364][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:07.365][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-12-20 12:39:07.366][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:07.367][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-12-20 12:39:07.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.381][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:07.384][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:07.385][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-12-20 12:39:07.387][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:07.388][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-12-20 12:39:07.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:07.405][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:07.406][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-12-20 12:39:07.407][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:07.409][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-12-20 12:39:07.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-12-20 12:39:07.428][biodb::testThat]
biodb.INFO [2024-12-20 12:39:07.429][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-12-20 12:39:07.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:07.431][biodb::testThat]
biodb.DEBUG[2024-12-20 12:39:07.434][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:07.439][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:07.440][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:07.442][private$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[2024-12-20 12:39:07.532][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[2024-12-20 12:39:07.618][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:07.621][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-12-20 12:39:07.625][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-12-20 12:39:07.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.643][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[2024-12-20 12:39:07.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:07.647][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:07.649][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-12-20 12:39:07.735][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-12-20 12:39:07.813][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:07.816][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-12-20 12:39:07.820][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-12-20 12:39:07.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:07.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-12-20 12:39:07.840][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-12-20 12:39:07.842][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-12-20 12:39:07.843][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-12-20 12:39:07.844][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-12-20 12:39:07.845][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:07.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:07.846][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:07.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:07.848][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-12-20 12:39:07.853][biodb::testContext]
biodb.INFO [2024-12-20 12:39:07.854][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 12:39:07.855][biodb::testContext] Test context - Test web services
biodb.INFO [2024-12-20 12:39:07.856][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 12:39:07.857][biodb::testContext]
biodb.INFO [2024-12-20 12:39:07.859][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-12-20 12:39:07.861][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-12-20 12:39:07.866][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:39:07.867][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-12-20 12:39:07.868][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-12-20 12:39:07.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.870][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[2024-12-20 12:39:07.871][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-12-20 12:39:07.872][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-12-20 12:39:07.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.876][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-12-20 12:39:07.877][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-12-20 12:39:07.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.880][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-12-20 12:39:07.881][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-12-20 12:39:07.881][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-12-20 12:39:07.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.884][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-12-20 12:39:07.885][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-12-20 12:39:07.886][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-12-20 12:39:07.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.889][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-12-20 12:39:07.890][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-12-20 12:39:07.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.893][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-12-20 12:39:07.894][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-12-20 12:39:07.895][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-12-20 12:39:07.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.898][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-12-20 12:39:07.898][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-12-20 12:39:07.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.901][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-12-20 12:39:07.902][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-12-20 12:39:07.903][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-12-20 12:39:07.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.906][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-12-20 12:39:07.907][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-12-20 12:39:07.908][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-12-20 12:39:07.909][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-12-20 12:39:07.910][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-12-20 12:39:07.910][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-12-20 12:39:07.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.913][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-12-20 12:39:07.914][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-12-20 12:39:07.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.917][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-12-20 12:39:07.918][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-12-20 12:39:07.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.921][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-12-20 12:39:07.922][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-12-20 12:39:07.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.925][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-12-20 12:39:07.926][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-12-20 12:39:07.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.929][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-12-20 12:39:07.930][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-12-20 12:39:07.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.933][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-12-20 12:39:07.933][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-12-20 12:39:07.949][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-12-20 12:39:07.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:07.953][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-12-20 12:39:07.953][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-12-20 12:39:07.954][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-12-20 12:39:07.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:07.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:07.957][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[2024-12-20 12:39:07.958][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-12-20 12:39:07.959][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:07.960][self$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[2024-12-20 12:39:07.961][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.962][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:07.963][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.964][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:07.965][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:07.965][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:07.966][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 12:39:07.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:07.968][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.969][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-12-20 12:39:07.969][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:07.970][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:07.971][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.972][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:39:07.972][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:39:07.972][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:39:07.972][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 12:39:07.972][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 12:39:07.973][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:07.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:07.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:07.975][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:07.976][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:07.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:07.977][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:07.978][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:07.979][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:07.980][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:07.980][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:07.981][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:07.982][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-12-20 12:39:07.984][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:07.985][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 12:39:07.986][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:07.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.988][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:07.989][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:07.990][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:07.990][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 12:39:07.991][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:07.992][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.993][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-12-20 12:39:07.994][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:07.994][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:07.995][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:07.996][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:39:07.996][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:39:07.996][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:39:07.996][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 12:39:07.996][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 12:39:07.997][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:07.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:07.999][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:07.999][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:08.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.003][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.004][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:08.005][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:08.006][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.006][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.007][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-12-20 12:39:08.009][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.010][self$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[2024-12-20 12:39:08.011][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.012][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:08.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.020][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.028][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.030][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.031][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 12:39:08.031][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:08.032][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.033][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-12-20 12:39:08.034][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:08.035][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.036][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.037][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.037][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:08.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.040][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:08.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.042][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.043][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.044][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:08.045][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:08.046][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.047][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.048][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-12-20 12:39:08.049][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.050][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 12:39:08.051][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.052][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:08.053][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.054][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.055][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.055][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.056][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 12:39:08.057][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:08.059][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.060][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-12-20 12:39:08.060][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:08.061][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.062][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.063][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.064][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:08.065][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.066][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.066][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:08.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.069][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.069][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.070][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:08.071][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:08.072][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.072][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.074][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:39:08.074][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.122][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[2024-12-20 12:39:08.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.137][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[2024-12-20 12:39:08.137][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-12-20 12:39:08.139][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-12-20 12:39:08.140][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-12-20 12:39:08.141][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-12-20 12:39:08.143][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 12:39:08.144][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-12-20 12:39:08.145][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-12-20 12:39:08.146][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-12-20 12:39:08.147][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-12-20 12:39:08.148][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-12-20 12:39:08.150][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 12:39:08.151][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-12-20 12:39:08.152][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-12-20 12:39:08.153][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-12-20 12:39:08.155][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-12-20 12:39:08.156][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-12-20 12:39:08.158][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-12-20 12:39:08.159][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-12-20 12:39:08.160][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 12:39:08.161][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-12-20 12:39:08.162][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-12-20 12:39:08.164][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-12-20 12:39:08.165][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-12-20 12:39:08.166][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-12-20 12:39:08.167][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-12-20 12:39:08.168][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-12-20 12:39:08.169][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-12-20 12:39:08.171][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-12-20 12:39:08.172][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-12-20 12:39:08.173][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-12-20 12:39:08.174][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-12-20 12:39:08.175][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-12-20 12:39:08.176][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-12-20 12:39:08.178][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-12-20 12:39:08.179][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-12-20 12:39:08.180][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-12-20 12:39:08.181][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-12-20 12:39:08.182][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-12-20 12:39:08.183][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-12-20 12:39:08.185][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-12-20 12:39:08.186][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-12-20 12:39:08.187][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-12-20 12:39:08.188][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-12-20 12:39:08.189][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-12-20 12:39:08.190][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-12-20 12:39:08.192][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-12-20 12:39:08.193][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-12-20 12:39:08.194][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-12-20 12:39:08.195][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-12-20 12:39:08.197][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-12-20 12:39:08.198][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-12-20 12:39:08.199][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-12-20 12:39:08.200][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-12-20 12:39:08.201][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-12-20 12:39:08.202][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-12-20 12:39:08.204][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-12-20 12:39:08.205][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-12-20 12:39:08.206][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-12-20 12:39:08.208][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-12-20 12:39:08.209][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-12-20 12:39:08.210][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-12-20 12:39:08.212][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-12-20 12:39:08.213][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-12-20 12:39:08.214][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-12-20 12:39:08.215][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-12-20 12:39:08.217][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-12-20 12:39:08.218][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 12:39:08.219][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 12:39:08.220][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-12-20 12:39:08.221][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-12-20 12:39:08.222][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-12-20 12:39:08.224][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-12-20 12:39:08.225][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-12-20 12:39:08.226][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-12-20 12:39:08.227][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-12-20 12:39:08.228][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-12-20 12:39:08.229][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-12-20 12:39:08.231][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-12-20 12:39:08.232][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-12-20 12:39:08.233][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-12-20 12:39:08.234][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-12-20 12:39:08.235][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-12-20 12:39:08.236][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-12-20 12:39:08.237][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-12-20 12:39:08.239][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-12-20 12:39:08.240][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:39:08.241][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.243][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.259][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[2024-12-20 12:39:08.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.263][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[2024-12-20 12:39:08.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.293][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[2024-12-20 12:39:08.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.316][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.DEBUG[2024-12-20 12:39:08.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.338][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-12-20 12:39:08.340][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-12-20 12:39:08.342][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.343][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.345][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:08.345][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.346][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.347][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.348][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-12-20 12:39:08.349][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-12-20 12:39:08.350][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:08.351][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.352][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-12-20 12:39:08.352][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-12-20 12:39:08.353][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-12-20 12:39:08.354][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.355][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:39:08.355][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:39:08.355][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:39:08.356][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-12-20 12:39:08.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.357][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.358][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:08.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.360][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.361][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:39:08.361][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-12-20 12:39:08.362][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:08.363][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:08.364][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.364][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-12-20 12:39:08.364][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-12-20 12:39:08.366][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 12:39:08.367][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 12:39:08.369][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-12-20 12:39:08.370][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 12:39:08.371][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 12:39:08.373][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 12:39:08.376][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-12-20 12:39:08.377][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-12-20 12:39:08.378][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-12-20 12:39:08.379][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-12-20 12:39:08.381][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 12:39:08.382][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 12:39:08.383][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-12-20 12:39:08.384][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-12-20 12:39:08.385][biodb::testThat]
biodb.INFO [2024-12-20 12:39:08.386][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-12-20 12:39:08.387][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:08.388][biodb::testThat]
biodb.DEBUG[2024-12-20 12:39:08.391][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-12-20 12:39:08.395][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:08.397][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-12-20 12:39:08.398][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:08.400][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-12-20 12:39:08.404][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-12-20 12:39:08.408][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:08.409][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:08.411][private$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[2024-12-20 12:39:08.497][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[2024-12-20 12:39:08.584][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:08.587][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-12-20 12:39:08.591][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-12-20 12:39:08.602][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-12-20 12:39:08.604][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-12-20 12:39:08.605][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-12-20 12:39:08.606][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-12-20 12:39:08.606][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:08.608][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.609][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-12-20 12:39:08.614][biodb::testContext]
biodb.INFO [2024-12-20 12:39:08.615][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 12:39:08.616][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-12-20 12:39:08.617][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-20 12:39:08.618][biodb::testContext]
biodb.INFO [2024-12-20 12:39:08.620][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-12-20 12:39:08.622][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-12-20 12:39:08.627][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:39:08.628][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-12-20 12:39:08.629][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-12-20 12:39:08.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.633][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-12-20 12:39:08.634][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-12-20 12:39:08.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.637][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-12-20 12:39:08.638][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-12-20 12:39:08.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.641][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-12-20 12:39:08.641][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-12-20 12:39:08.642][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-12-20 12:39:08.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.645][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-12-20 12:39:08.646][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-12-20 12:39:08.647][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-12-20 12:39:08.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.650][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-12-20 12:39:08.651][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-12-20 12:39:08.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.653][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[2024-12-20 12:39:08.654][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-12-20 12:39:08.655][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-12-20 12:39:08.655][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-12-20 12:39:08.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.658][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-12-20 12:39:08.659][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-12-20 12:39:08.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.662][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-12-20 12:39:08.663][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-12-20 12:39:08.664][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-12-20 12:39:08.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.667][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-12-20 12:39:08.668][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-12-20 12:39:08.668][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-12-20 12:39:08.669][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-12-20 12:39:08.670][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-12-20 12:39:08.671][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-12-20 12:39:08.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.674][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-12-20 12:39:08.675][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-12-20 12:39:08.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.678][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-12-20 12:39:08.678][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-12-20 12:39:08.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.681][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.DEBUG[2024-12-20 12:39:08.681][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-12-20 12:39:08.682][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-12-20 12:39:08.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.685][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-12-20 12:39:08.686][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-12-20 12:39:08.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.689][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-12-20 12:39:08.690][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-12-20 12:39:08.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.692][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-12-20 12:39:08.693][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-12-20 12:39:08.710][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-12-20 12:39:08.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.714][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-12-20 12:39:08.715][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-12-20 12:39:08.716][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-12-20 12:39:08.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.719][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-12-20 12:39:08.720][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.721][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-12-20 12:39:08.722][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.723][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:08.724][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.725][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.726][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.726][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.727][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 12:39:08.728][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:08.729][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.730][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-12-20 12:39:08.730][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:08.731][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.732][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.733][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:39:08.733][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:39:08.733][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:39:08.733][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 12:39:08.733][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 12:39:08.734][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:08.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.736][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:08.737][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.737][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.738][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.739][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.740][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:08.740][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:08.741][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.742][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.743][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-12-20 12:39:08.745][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.746][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 12:39:08.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.747][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:08.748][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.749][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.750][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.751][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.751][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 12:39:08.752][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:08.753][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.754][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-12-20 12:39:08.755][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:08.756][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.756][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.757][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:39:08.757][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:39:08.757][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:39:08.757][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-20 12:39:08.757][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-20 12:39:08.758][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:08.759][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.760][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.760][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:08.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.763][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.764][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.764][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:08.765][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:08.766][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.767][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.768][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-12-20 12:39:08.769][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.770][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-12-20 12:39:08.771][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.772][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:08.773][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.774][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.774][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.775][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.776][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-20 12:39:08.777][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:08.778][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.778][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-12-20 12:39:08.779][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:08.780][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.781][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.782][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.782][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:08.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.784][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.785][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:08.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.787][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.788][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.788][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:08.800][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:08.801][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.802][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.803][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-12-20 12:39:08.804][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.805][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-12-20 12:39:08.806][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.807][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:08.808][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.809][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.809][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.810][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.811][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-20 12:39:08.812][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:08.813][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.813][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-12-20 12:39:08.814][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:08.815][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.816][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:08.816][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.817][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-20 12:39:08.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.820][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:08.820][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:08.821][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:08.822][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:08.823][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.823][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:08.824][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:08.825][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:08.826][self$setPropertyValue]
biodb.DEBUG[2024-12-20 12:39:08.827][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:39:08.828][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.828][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[2024-12-20 12:39:08.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.843][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[2024-12-20 12:39:08.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.846][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[2024-12-20 12:39:08.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.850][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[2024-12-20 12:39:08.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.853][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[2024-12-20 12:39:08.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.857][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[2024-12-20 12:39:08.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.864][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[2024-12-20 12:39:08.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.886][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[2024-12-20 12:39:08.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.890][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-12-20 12:39:08.892][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-12-20 12:39:08.894][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-12-20 12:39:08.895][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-12-20 12:39:08.897][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 12:39:08.899][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-12-20 12:39:08.901][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-12-20 12:39:08.902][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-12-20 12:39:08.904][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-12-20 12:39:08.905][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-12-20 12:39:08.906][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 12:39:08.907][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-12-20 12:39:08.909][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-12-20 12:39:08.910][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-12-20 12:39:08.911][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-12-20 12:39:08.912][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-12-20 12:39:08.913][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-12-20 12:39:08.915][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-12-20 12:39:08.916][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 12:39:08.917][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-12-20 12:39:08.918][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-12-20 12:39:08.919][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-12-20 12:39:08.920][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-12-20 12:39:08.922][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-12-20 12:39:08.923][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-12-20 12:39:08.924][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-12-20 12:39:08.925][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-12-20 12:39:08.926][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-12-20 12:39:08.927][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-12-20 12:39:08.928][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-12-20 12:39:08.930][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-12-20 12:39:08.931][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-12-20 12:39:08.932][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-12-20 12:39:08.933][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-12-20 12:39:08.934][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-12-20 12:39:08.935][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-12-20 12:39:08.936][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-12-20 12:39:08.938][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-12-20 12:39:08.939][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-12-20 12:39:08.940][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-12-20 12:39:08.941][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-12-20 12:39:08.942][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-12-20 12:39:08.944][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-12-20 12:39:08.945][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-12-20 12:39:08.946][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-12-20 12:39:08.947][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-12-20 12:39:08.949][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-12-20 12:39:08.950][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-12-20 12:39:08.951][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-12-20 12:39:08.952][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-12-20 12:39:08.953][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-12-20 12:39:08.954][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-12-20 12:39:08.955][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-12-20 12:39:08.957][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-12-20 12:39:08.958][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-12-20 12:39:08.959][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-12-20 12:39:08.960][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-12-20 12:39:08.961][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-12-20 12:39:08.962][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-12-20 12:39:08.963][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-12-20 12:39:08.965][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-12-20 12:39:08.966][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-12-20 12:39:08.967][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-12-20 12:39:08.968][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-12-20 12:39:08.969][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-12-20 12:39:08.970][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-12-20 12:39:08.971][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 12:39:08.973][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 12:39:08.974][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-12-20 12:39:08.975][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-12-20 12:39:08.976][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-12-20 12:39:08.977][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-12-20 12:39:08.978][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-12-20 12:39:08.979][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-12-20 12:39:08.981][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-12-20 12:39:08.982][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-12-20 12:39:08.983][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-12-20 12:39:08.984][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-12-20 12:39:08.985][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-12-20 12:39:08.986][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-12-20 12:39:08.988][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-12-20 12:39:08.989][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-12-20 12:39:08.990][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-12-20 12:39:08.991][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-12-20 12:39:08.993][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-12-20 12:39:08.994][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-20 12:39:08.995][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:08.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:08.997][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:08.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:08.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:08.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:08.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.032][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[2024-12-20 12:39:09.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.042][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[2024-12-20 12:39:09.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-20 12:39:09.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.088][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[2024-12-20 12:39:09.090][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-12-20 12:39:09.092][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-12-20 12:39:09.094][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:09.095][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-12-20 12:39:09.095][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:09.096][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-20 12:39:09.097][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:09.098][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-20 12:39:09.099][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:09.099][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-12-20 12:39:09.100][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-12-20 12:39:09.101][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-20 12:39:09.102][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:09.103][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-12-20 12:39:09.103][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-12-20 12:39:09.104][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-12-20 12:39:09.105][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-12-20 12:39:09.106][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-20 12:39:09.106][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-20 12:39:09.106][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-20 12:39:09.107][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-12-20 12:39:09.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:09.108][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:09.109][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-20 12:39:09.110][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-20 12:39:09.111][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-20 12:39:09.111][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-20 12:39:09.112][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:39:09.112][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-12-20 12:39:09.113][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-20 12:39:09.114][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-20 12:39:09.114][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-12-20 12:39:09.115][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-12-20 12:39:09.115][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-12-20 12:39:09.116][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-20 12:39:09.118][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-20 12:39:09.119][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-12-20 12:39:09.120][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-20 12:39:09.121][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-20 12:39:09.123][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-20 12:39:09.126][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-12-20 12:39:09.127][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-12-20 12:39:09.128][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-12-20 12:39:09.130][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-12-20 12:39:09.131][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 12:39:09.131][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-20 12:39:09.133][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-12-20 12:39:09.133][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-12-20 12:39:09.135][biodb::testThat]
biodb.INFO [2024-12-20 12:39:09.136][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-12-20 12:39:09.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-20 12:39:09.137][biodb::testThat]
biodb.DEBUG[2024-12-20 12:39:09.140][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-12-20 12:39:09.144][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:09.145][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-12-20 12:39:09.146][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:09.148][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-12-20 12:39:09.151][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[2024-12-20 12:39:09.155][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-12-20 12:39:09.156][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-12-20 12:39:09.157][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-20 12:39:09.159][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-12-20 12:39:09.163][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-12-20 12:39:09.164][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-12-20 12:39:09.166][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-12-20 12:39:09.167][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-12-20 12:39:09.168][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-12-20 12:39:09.169][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-12-20 12:39:09.170][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-12-20 12:39:09.171][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-12-20 12:39:09.172][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-12-20 12:39:09.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:09.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-20 12:39:09.186][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-12-20 12:39:09.189][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-12-20 12:39:09.190][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-12-20 12:39:09.191][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-12-20 12:39:09.293][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-12-20 12:39:09.437][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-12-20 12:39:09.440][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-12-20 12:39:09.444][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-12-20 12:39:09.446][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-12-20 12:39:09.449][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-12-20 12:39:09.451][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-12-20 12:39:09.452][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-12-20 12:39:09.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-20 12:39:09.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-20 12:39:09.470][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:09.471][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:09.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.473][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:09.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:09.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.477][ef$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:09.478][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:09.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.480][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.481][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-12-20 12:39:09.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-12-20 12:39:09.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.484][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:09.485][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:09.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.487][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.488][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-20 12:39:09.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-20 12:39:09.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.491][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-20 12:39:09.492][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-20 12:39:09.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.494][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.495][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-20 12:39:09.496][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-20 12:39:09.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.498][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.499][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:09.500][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:09.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.501][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.502][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:09.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-20 12:39:09.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.506][ef$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:09.506][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:09.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.508][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.509][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-12-20 12:39:09.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-12-20 12:39:09.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.512][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:09.513][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:09.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.515][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:09.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-20 12:39:09.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.519][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:09.520][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:09.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.522][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-20 12:39:09.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-20 12:39:09.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.526][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:09.527][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:09.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.529][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.530][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-12-20 12:39:09.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-12-20 12:39:09.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.533][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:09.534][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:09.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.536][ef$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.537][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-20 12:39:09.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-20 12:39:09.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:09.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:09.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:09.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:09.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:09.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:09.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-20 12:39:09.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-20 12:39:09.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:09.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:09.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:09.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:09.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:09.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:09.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:09.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:09.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:09.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:09.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-20 12:39:09.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-20 12:39:09.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-20 12:39:09.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-20 12:39:09.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-20 12:39:09.574][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-12-20 12:39:09.578][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-12-20 12:39:09.580][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-12-20 12:39:09.581][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-12-20 12:39:09.581][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-12-20 12:39:09.582][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-20 12:39:09.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-20 12:39:09.584][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-20 12:39:09.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-20 12:39:09.585][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-12-20 12:39:09.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
> 
> proc.time()
   user  system elapsed 
 17.000   1.015  25.571

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	2.629	1.044	4.736
ChebiEntry	0.397	0.014	0.412