Multiple platform build/check report for BioC 3.21 - CHECK results for biodbChebi on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4783
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4552
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4581
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4533
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4463
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for biodbChebi on kjohnson3

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

raw results

Summary

Package: biodbChebi

Version: 1.13.0

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_1.13.0.tar.gz

StartedAt: 2025-03-26 18:16:29 -0400 (Wed, 26 Mar 2025)

EndedAt: 2025-03-26 18:17:43 -0400 (Wed, 26 Mar 2025)

EllapsedTime: 73.9 seconds

RetCode: 0

Status: OK

CheckDir: biodbChebi.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.13.0’
* 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/4.5-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.13.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 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 [2025-03-26 18:16:50.789][biodb::testContext]
biodb.INFO [2025-03-26 18:16:50.791][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 18:16:50.791][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-26 18:16:50.791][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 18:16:50.792][biodb::testContext]
biodb.INFO [2025-03-26 18:16:50.794][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 18:16:50.795][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 18:16:50.798][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:16:50.798][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 18:16:50.799][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 18:16:50.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.800][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 18:16:50.806][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 18:16:50.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.807][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 18:16:50.807][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 18:16:50.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.808][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 18:16:50.808][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 18:16:50.809][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 18:16:50.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.810][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 18:16:50.810][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 18:16:50.810][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 18:16:50.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.811][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 18:16:50.812][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 18:16:50.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.813][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 18:16:50.813][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 18:16:50.813][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 18:16:50.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.814][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 18:16:50.814][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 18:16:50.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.815][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 18:16:50.816][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 18:16:50.816][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 18:16:50.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.817][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 18:16:50.817][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 18:16:50.817][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 18:16:50.818][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 18:16:50.818][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 18:16:50.818][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 18:16:50.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.819][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 18:16:50.819][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 18:16:50.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.820][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 18:16:50.821][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 18:16:50.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.822][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 18:16:50.822][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 18:16:50.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.823][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 18:16:50.824][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 18:16:50.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.825][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 18:16:50.825][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 18:16:50.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.826][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 18:16:50.826][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 18:16:50.832][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 18:16:50.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.833][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 18:16:50.833][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 18:16:50.834][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 18:16:50.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.836][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 18:16:50.847][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.855][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-26 18:16:50.856][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.856][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:16:50.856][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.856][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.857][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.857][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.857][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 18:16:50.857][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:16:50.858][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.858][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 18:16:50.858][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:16:50.859][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.859][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.859][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:16:50.859][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:16:50.859][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:16:50.859][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 18:16:50.859][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 18:16:50.859][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:16:50.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:16:50.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:16:50.860][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:16:50.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:16:50.861][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:16:50.861][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.861][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.861][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:16:50.862][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:16:50.862][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.862][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.862][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 18:16:50.863][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.863][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 18:16:50.863][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.864][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:16:50.864][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.864][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.864][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.865][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.865][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 18:16:50.865][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:16:50.865][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.866][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 18:16:50.866][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:16:50.866][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.866][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.867][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:16:50.867][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:16:50.867][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:16:50.867][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 18:16:50.867][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 18:16:50.867][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:16:50.867][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:16:50.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:16:50.868][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:16:50.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:16:50.868][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:16:50.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.869][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.869][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:16:50.869][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:16:50.869][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.870][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.870][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 18:16:50.870][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.871][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-26 18:16:50.871][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.871][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:16:50.871][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.872][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.872][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.872][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.872][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 18:16:50.873][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:16:50.873][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.873][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 18:16:50.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:16:50.874][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.874][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.874][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.874][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:16:50.875][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:16:50.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:16:50.875][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:16:50.875][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:16:50.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:16:50.876][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.876][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.876][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:16:50.876][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:16:50.877][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.877][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.877][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 18:16:50.878][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.878][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 18:16:50.878][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.878][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:16:50.879][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.879][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.879][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.879][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.880][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 18:16:50.880][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:16:50.880][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.880][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 18:16:50.881][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:16:50.881][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.881][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.881][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.882][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:16:50.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:16:50.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:16:50.882][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:16:50.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:16:50.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:16:50.883][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.883][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.884][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:16:50.884][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:16:50.884][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.884][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:16:50.886][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:16:50.886][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.886][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[2025-03-26 18:16:50.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.889][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[2025-03-26 18:16:50.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.891][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[2025-03-26 18:16:50.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.892][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[2025-03-26 18:16:50.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.897][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[2025-03-26 18:16:50.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.901][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[2025-03-26 18:16:50.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.903][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[2025-03-26 18:16:50.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.906][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[2025-03-26 18:16:50.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.908][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 18:16:50.910][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 18:16:50.911][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 18:16:50.911][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 18:16:50.911][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 18:16:50.912][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 18:16:50.912][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 18:16:50.912][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 18:16:50.913][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 18:16:50.913][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 18:16:50.914][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 18:16:50.914][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 18:16:50.914][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 18:16:50.915][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 18:16:50.915][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 18:16:50.915][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 18:16:50.916][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 18:16:50.916][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 18:16:50.916][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 18:16:50.917][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 18:16:50.917][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 18:16:50.917][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 18:16:50.918][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 18:16:50.918][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 18:16:50.919][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 18:16:50.919][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 18:16:50.919][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 18:16:50.920][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 18:16:50.920][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 18:16:50.920][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 18:16:50.921][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 18:16:50.921][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 18:16:50.921][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 18:16:50.922][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 18:16:50.922][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 18:16:50.923][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 18:16:50.923][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 18:16:50.923][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 18:16:50.924][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 18:16:50.924][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 18:16:50.924][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 18:16:50.925][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 18:16:50.925][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 18:16:50.925][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 18:16:50.926][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 18:16:50.926][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 18:16:50.926][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 18:16:50.927][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 18:16:50.927][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 18:16:50.928][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 18:16:50.928][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 18:16:50.928][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 18:16:50.929][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 18:16:50.929][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 18:16:50.929][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 18:16:50.930][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 18:16:50.930][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 18:16:50.930][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 18:16:50.931][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 18:16:50.931][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 18:16:50.931][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 18:16:50.932][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 18:16:50.932][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 18:16:50.933][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 18:16:50.933][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 18:16:50.933][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 18:16:50.934][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 18:16:50.934][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 18:16:50.934][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 18:16:50.935][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 18:16:50.935][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 18:16:50.935][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 18:16:50.936][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 18:16:50.936][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 18:16:50.936][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 18:16:50.937][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 18:16:50.937][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 18:16:50.938][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 18:16:50.938][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 18:16:50.938][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 18:16:50.939][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 18:16:50.939][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 18:16:50.939][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 18:16:50.941][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 18:16:50.942][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 18:16:50.943][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:16:50.943][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.944][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.944][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[2025-03-26 18:16:50.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.947][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.DEBUG[2025-03-26 18:16:50.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.954][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[2025-03-26 18:16:50.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.957][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[2025-03-26 18:16:50.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.959][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[2025-03-26 18:16:50.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.964][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[2025-03-26 18:16:50.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.971][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[2025-03-26 18:16:50.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:50.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:16:50.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:50.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:50.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:50.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:50.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:50.974][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[2025-03-26 18:16:50.975][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-26 18:16:50.978][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-26 18:16:50.979][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.979][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.980][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.980][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:16:50.980][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.980][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.981][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.981][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-26 18:16:50.981][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 18:16:50.982][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:16:50.982][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.982][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-26 18:16:50.982][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:16:50.983][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 18:16:50.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:16:50.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:16:50.984][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:16:50.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:16:50.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:16:50.985][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:16:50.985][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:16:50.985][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-26 18:16:50.985][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:16:50.986][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:16:50.986][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 18:16:50.986][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-26 18:16:50.986][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-26 18:16:50.988][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 18:16:50.989][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 18:16:50.989][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-26 18:16:50.989][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 18:16:50.990][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 18:16:50.990][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 18:16:51.001][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-26 18:16:51.001][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-26 18:16:51.003][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-26 18:16:51.004][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-26 18:16:51.021][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 18:16:51.022][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 18:16:51.022][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-26 18:16:51.022][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-26 18:16:51.026][biodb::testThat]
biodb.INFO [2025-03-26 18:16:51.027][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-26 18:16:51.027][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:16:51.027][biodb::testThat]
biodb.TRACE[2025-03-26 18:16:51.029][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-26 18:16:51.030][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:16:51.031][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:16:51.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:51.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:51.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:51.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:51.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:51.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:51.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:51.045][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.045][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.051][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:51.052][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:51.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.061][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:51.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:51.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.062][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:51.062][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:51.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.063][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.063][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:51.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:51.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.064][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.064][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.066][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.067][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.067][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.069][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.069][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.069][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.070][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.071][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:51.071][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.072][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.072][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:51.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.073][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.073][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.074][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.075][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.075][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.076][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.081][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:51.082][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.082][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.082][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:51.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.083][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:51.084][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:51.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.084][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.084][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:51.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:51.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:51.106][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-26 18:16:51.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.123][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.124][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.125][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-26 18:16:51.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-26 18:16:51.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.126][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-26 18:16:51.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-26 18:16:51.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.158][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.159][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.169][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.169][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.170][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.176][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.177][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.177][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.178][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.178][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.182][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:51.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:51.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.183][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:51.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:51.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:51.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:51.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.185][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:51.185][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:51.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.186][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.186][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:51.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:51.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.192][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.193][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.200][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.201][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.205][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:51.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:51.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.206][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:51.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:51.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.207][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:51.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:51.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.208][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:51.208][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:51.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.209][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.212][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:51.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:51.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.215][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.217][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.218][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.219][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.219][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.220][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.224][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.225][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.226][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.227][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.227][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.228][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.228][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.231][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:51.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:51.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.232][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:51.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:51.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.233][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:51.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:51.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.235][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:51.235][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:51.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.235][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.236][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:51.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:51.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.241][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.242][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.243][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.243][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.243][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.250][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.251][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.258][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.258][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.259][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.260][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:51.260][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:51.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.262][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:51.263][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:51.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.265][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.265][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.266][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.267][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.268][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.269][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.270][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.270][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.272][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.272][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.273][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.274][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.274][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.275][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.276][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.276][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.277][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.278][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.279][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.279][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.281][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:51.281][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:51.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.281][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 18:16:51.284][biodb::testThat]
biodb.INFO [2025-03-26 18:16:51.284][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-26 18:16:51.284][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:16:51.285][biodb::testThat]
biodb.DEBUG[2025-03-26 18:16:51.289][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-26 18:16:51.292][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:16:51.294][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-26 18:16:51.294][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:16:51.294][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-26 18:16:51.295][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:16:51.304][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:16:51.305][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:16:51.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:51.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:51.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:51.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:51.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:51.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:51.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:51.309][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.310][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.310][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.317][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:51.317][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:51.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.318][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.318][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:51.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:51.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.319][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:51.319][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:51.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.320][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.320][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:51.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:51.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.321][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.321][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.322][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.323][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.323][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.324][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.325][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.325][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.326][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.326][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:51.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.327][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:51.328][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.328][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.328][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:51.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.329][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.330][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.331][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.332][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.332][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.334][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:51.334][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.335][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:51.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:51.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.336][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:51.336][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:51.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.336][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.337][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:51.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:51.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:51.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:51.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:51.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:51.350][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-26 18:16:51.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-26 18:16:51.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-26 18:16:51.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-26 18:16:51.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-26 18:16:51.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-26 18:16:51.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-26 18:16:51.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 18:16:51.356][biodb::testThat]
biodb.INFO [2025-03-26 18:16:51.356][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-26 18:16:51.356][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:16:51.357][biodb::testThat]
biodb.TRACE[2025-03-26 18:16:51.357][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.358][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.358][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:51.359][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-26 18:16:51.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:51.371][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-26 18:16:51.373][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-26 18:16:51.379][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:16:51.386][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-26 18:16:51.387][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:16:51.387][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-26 18:16:51.394][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:16:51.396][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:16:51.396][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 18:16:51.396][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:16:51.397][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-26 18:16:51.398][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-26 18:16:51.402][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.402][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:51.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.403][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.403][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.403][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.404][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 18:16:51.405][biodb::testThat]
biodb.INFO [2025-03-26 18:16:51.405][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-26 18:16:51.406][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:16:51.406][biodb::testThat]
biodb.TRACE[2025-03-26 18:16:51.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:51.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:51.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:51.437][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:16:51.438][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:16:51.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 18:16:51.439][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:16:51.440][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-26 18:16:51.445][biodb::testThat]
biodb.INFO [2025-03-26 18:16:51.445][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-26 18:16:51.445][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:16:51.446][biodb::testThat]
biodb.TRACE[2025-03-26 18:16:51.452][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.453][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.455][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.458][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.459][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.460][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-26 18:16:51.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-26 18:16:51.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.461][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-26 18:16:51.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-26 18:16:51.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:51.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:51.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:51.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:51.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.477][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.478][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 18:16:51.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.479][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-26 18:16:51.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-26 18:16:51.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:51.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-26 18:16:51.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-26 18:16:51.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:51.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 18:16:51.483][biodb::testThat]
biodb.INFO [2025-03-26 18:16:51.483][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-26 18:16:51.484][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:16:51.484][biodb::testThat]
biodb.INFO [2025-03-26 18:16:51.487][biodb::testThat]
biodb.INFO [2025-03-26 18:16:51.487][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-26 18:16:51.487][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:16:51.488][biodb::testThat]
biodb.INFO [2025-03-26 18:16:51.490][biodb::testThat]
biodb.INFO [2025-03-26 18:16:51.491][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-26 18:16:51.491][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:16:51.491][biodb::testThat]
biodb.DEBUG[2025-03-26 18:16:51.492][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-26 18:16:52.481][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-26 18:16:53.503][biodb::testThat]
biodb.INFO [2025-03-26 18:16:53.504][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-26 18:16:53.504][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:16:53.504][biodb::testThat]
biodb.DEBUG[2025-03-26 18:16:53.868][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-03-26 18:16:54.221][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:54.222][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:54.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.222][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:54.222][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:54.223][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:54.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.223][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 18:16:54.224][biodb::testThat]
biodb.INFO [2025-03-26 18:16:54.224][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-03-26 18:16:54.225][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:16:54.225][biodb::testThat]
biodb.TRACE[2025-03-26 18:16:54.229][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:54.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:54.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:54.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:54.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:54.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:54.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:54.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:54.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:54.267][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:16:54.268][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:16:54.269][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 18:16:54.269][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:16:54.270][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-26 18:16:54.293][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:16:54.294][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:16:54.295][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 18:16:54.295][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:16:54.296][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-26 18:16:54.301][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 18:16:54.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 18:16:54.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:54.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:54.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:54.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:54.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:54.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:54.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:54.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:54.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:54.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:54.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:54.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:54.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:54.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:54.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:54.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:54.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:54.315][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:16:54.317][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:16:54.317][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-26 18:16:54.317][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:16:54.318][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-26 18:16:54.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:54.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:54.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:54.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:54.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:54.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:54.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:54.323][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-26 18:16:54.339][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:16:54.339][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-26 18:16:54.340][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:16:54.340][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:16:54.341][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:16:54.341][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:16:54.341][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:16:54.341][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:16:54.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:54.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:54.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:54.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:54.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:54.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:54.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:54.349][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-26 18:16:54.350][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:16:54.350][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:16:54.350][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-26 18:16:54.697][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-26 18:16:55.033][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:16:55.034][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-26 18:16:55.039][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-26 18:16:55.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-26 18:16:55.040][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:16:55.041][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:16:55.041][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:16:55.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:55.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:55.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:55.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:55.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:55.044][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:55.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:55.046][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.046][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.046][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.048][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:55.048][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:55.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.049][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.049][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:55.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:55.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.050][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:55.050][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:55.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.051][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.051][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:55.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:55.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.052][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:55.053][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:55.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:55.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:55.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.054][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:55.055][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:55.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.055][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:55.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:55.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.060][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:55.060][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:55.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.061][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.061][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:55.061][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.062][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.062][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:55.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.063][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:55.063][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:55.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:55.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:55.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.065][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:55.066][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:55.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.066][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.067][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:55.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:55.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.068][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:55.068][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:55.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.068][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.069][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:55.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:55.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.070][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:55.070][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:55.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.070][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.071][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:55.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:55.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:55.082][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-26 18:16:55.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:55.091][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:16:55.092][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:16:55.092][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-26 18:16:55.093][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:16:55.093][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-26 18:16:55.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:55.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:55.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:55.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:55.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:55.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:55.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:55.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:55.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:55.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:55.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:55.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:55.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:55.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:55.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:55.108][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-26 18:16:55.109][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:16:55.109][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-26 18:16:55.110][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:16:55.110][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:16:55.110][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:16:55.110][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:16:55.111][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:16:55.111][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:16:55.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:55.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:55.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:55.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:55.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:55.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:55.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:55.121][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-26 18:16:55.126][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:16:55.127][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:16:55.131][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-26 18:16:55.503][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-26 18:16:55.832][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:16:55.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-26 18:16:55.834][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-26 18:16:55.835][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-26 18:16:55.835][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:16:55.835][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:16:55.836][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:16:55.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:55.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:55.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:55.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:55.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:55.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:55.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:55.840][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.841][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.841][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.843][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:55.843][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:55.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:55.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:55.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.848][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:55.848][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:55.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.849][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.849][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:55.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:55.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.850][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:55.851][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:55.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.851][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:55.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:55.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.853][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:55.853][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:55.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.853][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:55.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:55.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.855][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:55.855][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:55.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.855][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.856][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:55.856][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.857][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:55.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.858][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:55.858][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:55.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.859][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:55.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:55.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.860][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:55.860][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:55.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:55.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:55.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.862][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:55.862][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:55.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.863][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.863][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:55.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:55.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.864][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:55.865][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:55.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.865][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:55.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:55.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:55.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:55.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:55.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:55.879][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-26 18:16:55.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:55.888][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:16:55.889][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:16:55.890][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 18:16:55.890][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:16:55.890][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-26 18:16:55.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:55.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:55.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:55.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:55.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:55.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:55.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:55.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:55.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:55.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:55.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:55.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:55.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:55.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:55.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:55.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:55.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:55.901][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[2025-03-26 18:16:55.901][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-26 18:16:55.901][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:16:55.917][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-26 18:16:55.917][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:16:55.917][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:16:55.918][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:16:55.918][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:16:55.918][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:16:55.919][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:16:55.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:55.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:55.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:55.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:55.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:55.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:55.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:55.923][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-26 18:16:55.924][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:16:55.924][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:16:55.925][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-26 18:16:56.464][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-26 18:16:56.792][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:16:56.793][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-26 18:16:56.795][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-26 18:16:56.796][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-26 18:16:56.796][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:16:56.797][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:16:56.797][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:16:56.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:56.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:56.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:56.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:56.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:56.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:56.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:56.802][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:56.802][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:56.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:56.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:56.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.805][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:56.805][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:56.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.805][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.806][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:56.806][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:56.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.807][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.807][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:56.807][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:56.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.808][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.808][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:56.808][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:56.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.809][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.809][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:56.810][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:56.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.810][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.810][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:56.811][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.811][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.812][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:56.812][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:56.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.812][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.813][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:56.813][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:56.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:56.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:56.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.815][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:56.819][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:56.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.821][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.821][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:56.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:56.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.822][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:56.823][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:56.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.823][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:56.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:56.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:56.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:56.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:56.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:56.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:56.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:56.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:56.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:56.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:56.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:56.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:56.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:56.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:56.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:56.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:56.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:56.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:56.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:56.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:56.834][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-26 18:16:56.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:56.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:56.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:56.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:56.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:56.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:56.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:56.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:56.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:56.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:56.843][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[2025-03-26 18:16:56.843][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-26 18:16:56.843][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:16:56.844][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-26 18:16:56.844][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:16:56.845][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:16:56.845][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:16:56.845][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:16:56.845][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:16:56.846][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:16:56.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:56.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:56.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:56.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:56.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:56.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:56.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:56.853][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-26 18:16:56.854][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:16:56.854][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:16:56.854][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-26 18:16:57.192][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-26 18:16:57.521][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:16:57.522][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-26 18:16:57.523][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-26 18:16:57.524][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-26 18:16:57.525][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:16:57.525][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:16:57.525][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:16:57.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:57.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:57.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:57.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:57.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:57.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:57.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:57.530][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:57.530][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:57.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:57.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:57.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.532][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:57.532][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:57.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.533][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:57.533][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:57.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.534][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:57.534][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:57.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.535][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.535][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:57.535][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:57.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.536][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.536][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:57.537][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:57.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.537][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:57.538][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.538][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.538][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:57.539][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:57.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.539][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.539][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:57.540][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:57.540][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.540][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:57.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:57.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.542][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:57.542][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:57.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.543][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:57.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:57.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.544][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:57.544][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:57.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.545][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:57.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:57.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:57.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:57.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:57.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:57.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:57.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:57.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:57.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:57.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:57.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:57.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:57.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:57.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:57.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:57.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:57.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:57.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:57.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:57.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:57.559][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-26 18:16:57.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:57.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:57.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:57.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:57.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:57.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:57.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:57.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:57.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:57.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:57.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:57.567][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-26 18:16:57.568][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:16:57.568][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-26 18:16:57.569][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:16:57.569][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:16:57.569][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:16:57.569][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:16:57.570][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:16:57.570][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:16:57.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:57.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:57.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:57.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:57.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:57.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:57.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:57.574][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-26 18:16:57.575][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:16:57.575][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:16:57.577][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-26 18:16:57.921][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-26 18:16:58.250][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:16:58.251][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-26 18:16:58.252][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-26 18:16:58.252][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-26 18:16:58.253][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:16:58.253][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:16:58.254][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:16:58.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:58.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:58.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:58.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:58.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:58.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:58.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:58.258][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:58.258][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:58.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.259][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:58.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:58.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.260][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:58.261][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:58.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.261][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:58.262][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:58.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.262][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.263][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:58.263][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:58.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.264][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:58.264][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:58.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.264][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.265][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:58.265][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:58.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.265][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.266][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:58.266][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.267][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.267][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:58.267][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:58.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.268][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:58.268][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:58.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.269][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:58.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:58.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.270][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:58.270][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:58.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.271][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.271][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:58.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:58.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.272][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:58.273][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:58.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.273][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:58.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:58.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:58.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:58.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:58.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:58.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:58.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:58.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:58.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:58.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:58.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:58.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:58.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:58.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:58.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:58.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:58.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:58.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:58.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:58.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:58.287][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-26 18:16:58.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:58.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:58.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:58.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:58.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:58.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:58.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:58.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:58.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:58.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:58.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:58.296][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-26 18:16:58.296][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:16:58.297][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-26 18:16:58.297][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:16:58.297][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:16:58.297][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:16:58.298][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:16:58.298][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:16:58.298][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:16:58.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:58.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:58.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:58.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:58.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:58.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:58.302][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.DEBUG[2025-03-26 18:16:58.302][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-26 18:16:58.303][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:16:58.304][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:16:58.304][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-26 18:16:58.655][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-26 18:16:58.996][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:16:58.997][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-26 18:16:58.998][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-26 18:16:59.001][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-26 18:16:59.003][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:16:59.003][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:16:59.003][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:16:59.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:59.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:59.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:59.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:59.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:59.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:59.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:59.008][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.008][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.009][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.010][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:59.010][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:59.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.011][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.011][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:59.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:59.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.012][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:59.012][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:59.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.013][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.013][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:59.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:59.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.014][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:59.015][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:59.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.015][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:59.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:59.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.016][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:59.017][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:59.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.017][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:59.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:59.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.018][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:59.019][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:59.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.019][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.019][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:59.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:59.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.021][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:59.021][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.021][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.022][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:59.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.023][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:59.023][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:59.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:59.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:59.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.025][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:59.025][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:59.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.025][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:59.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:59.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.027][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:59.027][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:59.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.028][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:59.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:59.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.031][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:59.032][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:59.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.032][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.032][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:59.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:59.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:59.043][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-26 18:16:59.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:59.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:59.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:59.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:59.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:59.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:59.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:59.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:59.050][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-26 18:16:59.050][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:16:59.051][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-26 18:16:59.051][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:16:59.051][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:16:59.052][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:16:59.052][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:16:59.052][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:16:59.052][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:16:59.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:59.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:59.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:59.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:59.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:59.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:59.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:59.056][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-26 18:16:59.059][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:16:59.060][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:16:59.060][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-26 18:16:59.407][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-26 18:16:59.741][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:16:59.742][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-26 18:16:59.743][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-26 18:16:59.744][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-26 18:16:59.745][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:16:59.745][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:16:59.745][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:16:59.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:59.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:59.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:59.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:59.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:59.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:59.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:16:59.750][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.750][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.751][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.752][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:59.753][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:59.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.753][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.754][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:16:59.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:16:59.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.755][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:59.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:59.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.756][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:16:59.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:16:59.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.757][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:59.757][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:59.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.758][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:16:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:16:59.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.759][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:59.760][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:59.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.760][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:16:59.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:16:59.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.761][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:59.762][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:59.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.762][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.763][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:59.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:16:59.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.764][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:59.764][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.764][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.765][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:16:59.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.766][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:59.766][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:59.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.767][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:59.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:16:59.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.772][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:59.772][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:59.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.773][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:16:59.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:16:59.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.775][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:59.775][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:59.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.775][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.776][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:16:59.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:16:59.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.777][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:59.777][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:59.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.778][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.778][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:16:59.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:16:59.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:16:59.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:16:59.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:16:59.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:59.790][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-26 18:16:59.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:16:59.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:16:59.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:16:59.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:16:59.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:59.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:59.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:59.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:59.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:59.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:59.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:59.797][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-26 18:16:59.797][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:16:59.797][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-26 18:16:59.798][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:16:59.798][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:16:59.798][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:16:59.799][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:16:59.801][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:16:59.802][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:16:59.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:16:59.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:16:59.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:16:59.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:16:59.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:16:59.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:16:59.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:16:59.807][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-26 18:16:59.808][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:16:59.808][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:16:59.808][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-26 18:17:00.146][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-26 18:17:00.480][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-03-26 18:17:00.481][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-26 18:17:00.481][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-26 18:17:00.483][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-26 18:17:00.484][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-26 18:17:00.484][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:00.484][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:00.485][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:00.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:00.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:00.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:00.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:00.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:00.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:00.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:00.490][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:00.490][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:00.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.491][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:00.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:00.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.492][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:00.492][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:00.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.493][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.493][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:00.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:00.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.494][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:00.495][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:00.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.495][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:00.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:00.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.497][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:00.497][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:00.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:00.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:00.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.499][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:00.499][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:00.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.500][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.500][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:00.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:00.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.501][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:00.501][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:00.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.502][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.502][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:00.503][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:00.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.503][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.506][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:00.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:00.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.509][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:00.509][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:00.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.510][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:00.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:00.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.511][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:00.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:00.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.512][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:00.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:00.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.513][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:00.514][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:00.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.514][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:00.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:00.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.515][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:00.516][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:00.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.516][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.516][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:00.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:00.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:00.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:00.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:00.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:00.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:00.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:00.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:00.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:00.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:00.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:00.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:00.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:00.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:00.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:00.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:00.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:00.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:00.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:00.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:00.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:00.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:00.527][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-26 18:17:00.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:00.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:00.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:00.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:00.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:00.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:00.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:00.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:00.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:00.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:00.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:00.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:00.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:00.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:00.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:00.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:00.536][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-26 18:17:00.537][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:00.537][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-26 18:17:00.538][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:00.538][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:00.538][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:00.538][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:00.539][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:00.539][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:00.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:00.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:00.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:00.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:00.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:00.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:00.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:00.543][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-26 18:17:00.544][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:00.544][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:00.545][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-26 18:17:00.898][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-26 18:17:01.233][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-03-26 18:17:01.234][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-26 18:17:01.234][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-26 18:17:01.236][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-26 18:17:01.237][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-26 18:17:01.238][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:01.238][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:01.238][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:01.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:01.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:01.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:01.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:01.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:01.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:01.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:01.243][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.243][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.244][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.245][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:01.246][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:01.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.246][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.247][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:01.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:01.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.248][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:01.248][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:01.248][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.248][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.249][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:01.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:01.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.250][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:01.250][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:01.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:01.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:01.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.252][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:01.252][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:01.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.253][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:01.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:01.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.259][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:01.259][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:01.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.260][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.260][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:01.261][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:01.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.261][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:01.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:01.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.263][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:01.263][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:01.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:01.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:01.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.265][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:01.265][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:01.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.266][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:01.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:01.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.269][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:01.269][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:01.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.270][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.270][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:01.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:01.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.273][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:01.273][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:01.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.273][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.274][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:01.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:01.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:01.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:01.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:01.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:01.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:01.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:01.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:01.286][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-26 18:17:01.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:01.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:01.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:01.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:01.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:01.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:01.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:01.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:01.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:01.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:01.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:01.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:01.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:01.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:01.297][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-26 18:17:01.297][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:01.298][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-26 18:17:01.298][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:01.298][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:01.299][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:01.299][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:01.299][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:01.299][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:01.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:01.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:01.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:01.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:01.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:01.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:01.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:01.304][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-26 18:17:01.305][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:01.305][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:01.305][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-26 18:17:01.650][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-26 18:17:01.984][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:01.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-26 18:17:01.986][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-26 18:17:01.987][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-26 18:17:01.988][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:01.989][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:01.989][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:01.990][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:01.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:01.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:01.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:01.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:01.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:01.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:01.994][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.994][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.994][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:01.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:01.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.996][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:01.996][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:01.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.997][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.997][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:01.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:01.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.998][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:01.999][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:01.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:01.999][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:01.999][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:02.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:02.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.001][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:02.005][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:02.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.006][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:02.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:02.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.007][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:02.008][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:02.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.008][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:02.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:02.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.009][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:02.010][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:02.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.010][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.011][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:02.011][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:02.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.011][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.012][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:02.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:02.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.013][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:02.013][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:02.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.014][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:02.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:02.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.015][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:02.015][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:02.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.016][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:02.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:02.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.017][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:02.017][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:02.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.018][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.018][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:02.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:02.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.019][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:02.020][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:02.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.020][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:02.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:02.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:02.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:02.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:02.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:02.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:02.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:02.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:02.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:02.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:02.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:02.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:02.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:02.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:02.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:02.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:02.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:02.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:02.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:02.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:02.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:02.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:02.035][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-26 18:17:02.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:02.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:02.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:02.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:02.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:02.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:02.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:02.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:02.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:02.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:02.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:02.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:02.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:02.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:02.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:02.042][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[2025-03-26 18:17:02.043][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-26 18:17:02.043][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:02.043][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-26 18:17:02.044][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:02.044][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:02.045][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:02.045][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:02.045][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:02.045][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:02.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:02.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:02.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:02.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:02.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:02.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:02.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:02.050][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-26 18:17:02.051][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:02.052][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:02.052][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-26 18:17:02.760][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-26 18:17:03.095][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:03.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-26 18:17:03.097][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-26 18:17:03.098][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-26 18:17:03.098][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:03.098][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:03.099][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:03.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:03.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:03.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:03.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:03.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:03.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:03.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:03.103][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.104][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.104][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.106][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:03.106][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:03.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.107][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:03.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:03.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.113][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:03.113][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:03.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.114][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.114][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:03.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:03.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.116][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:03.116][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:03.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.117][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:03.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:03.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.119][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:03.119][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:03.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.128][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:03.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:03.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.129][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:03.130][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:03.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.131][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:03.131][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.131][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.132][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:03.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.133][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:03.133][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:03.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.134][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:03.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:03.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.135][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:03.136][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:03.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.136][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:03.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:03.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.138][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:03.138][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:03.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.139][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:03.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:03.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.140][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:03.140][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:03.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.141][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.141][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:03.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:03.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:03.156][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-26 18:17:03.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:03.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:03.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:03.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:03.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:03.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:03.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:03.162][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.DEBUG[2025-03-26 18:17:03.163][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-26 18:17:03.163][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:03.163][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-26 18:17:03.164][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:03.164][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:03.164][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:03.164][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:03.165][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:03.165][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:03.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:03.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:03.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:03.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:03.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:03.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:03.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:03.169][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-26 18:17:03.170][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:03.170][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:03.170][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-26 18:17:03.508][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-26 18:17:03.841][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:03.842][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-26 18:17:03.844][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-26 18:17:03.844][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-26 18:17:03.845][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:03.845][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:03.846][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:03.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:03.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:03.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:03.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:03.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:03.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:03.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:03.857][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.857][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.858][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.860][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:03.860][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:03.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.860][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.861][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:03.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:03.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.862][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:03.862][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:03.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.863][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.863][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:03.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:03.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.864][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:03.864][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:03.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.865][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:03.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:03.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.866][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:03.867][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:03.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.867][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:03.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:03.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.869][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:03.869][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:03.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.870][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:03.870][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.871][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:03.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.872][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:03.872][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:03.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.873][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:03.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:03.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.874][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:03.874][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:03.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.875][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:03.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:03.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.876][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:03.876][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:03.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.877][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.877][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:03.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:03.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.878][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:03.879][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:03.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.879][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:03.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:03.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:03.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:03.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:03.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:03.894][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-26 18:17:03.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:03.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:03.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:03.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:03.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:03.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:03.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:03.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:03.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:03.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:03.901][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[2025-03-26 18:17:03.901][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-26 18:17:03.901][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:03.902][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-26 18:17:03.902][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:03.903][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:03.903][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:03.903][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:03.904][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:03.904][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:03.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:03.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:03.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:03.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:03.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:03.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:03.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:03.908][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-26 18:17:03.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:03.909][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:03.910][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-26 18:17:04.239][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-26 18:17:04.571][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:04.572][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-26 18:17:04.574][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-26 18:17:04.575][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-26 18:17:04.575][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:04.583][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:04.583][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:04.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:04.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:04.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:04.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:04.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:04.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:04.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:04.590][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:04.590][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:04.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.591][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:04.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:04.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.592][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:04.593][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:04.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.593][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.594][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:04.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:04.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.595][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:04.595][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:04.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.596][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:04.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:04.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.597][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:04.597][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:04.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.598][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.598][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:04.598][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:04.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.599][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:04.600][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:04.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.600][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.600][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:04.601][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:04.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.601][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.601][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:04.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:04.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:04.603][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:04.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.603][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:04.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:04.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.605][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:04.605][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:04.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.606][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:04.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:04.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.607][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:04.607][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:04.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.608][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.608][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:04.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:04.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.609][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:04.610][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:04.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.610][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:04.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:04.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:04.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:04.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:04.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:04.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:04.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:04.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:04.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:04.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:04.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:04.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:04.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:04.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:04.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:04.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:04.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:04.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:04.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:04.631][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-26 18:17:04.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:04.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:04.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:04.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:04.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:04.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:04.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:04.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:04.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:04.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:04.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:04.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:04.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:04.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:04.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:04.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:04.639][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-26 18:17:04.640][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:04.640][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-26 18:17:04.641][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:04.641][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:04.641][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:04.642][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:04.642][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:04.642][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:04.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:04.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:04.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:04.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:04.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:04.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:04.646][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[2025-03-26 18:17:04.647][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-26 18:17:04.648][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:04.648][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:04.648][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-26 18:17:04.984][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-26 18:17:05.313][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:05.314][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-26 18:17:05.315][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-26 18:17:05.316][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-26 18:17:05.316][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:05.316][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:05.317][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:05.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:05.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:05.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:05.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:05.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:05.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:05.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:05.325][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:05.325][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:05.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.326][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:05.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:05.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.327][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:05.328][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:05.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.328][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.328][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:05.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:05.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.329][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:05.330][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:05.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.331][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:05.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:05.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.332][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:05.332][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:05.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.332][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.333][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:05.333][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:05.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.333][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.334][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:05.334][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:05.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.335][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:05.335][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:05.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.336][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:05.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:05.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.337][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:05.337][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:05.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.338][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:05.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:05.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.339][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:05.339][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:05.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.340][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:05.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:05.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.341][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:05.341][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:05.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.342][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.342][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:05.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:05.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.343][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:05.343][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:05.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.344][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:05.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:05.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:05.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:05.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:05.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:05.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:05.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:05.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:05.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:05.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:05.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:05.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:05.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:05.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:05.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:05.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:05.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:05.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:05.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:05.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:05.357][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-26 18:17:05.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:05.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:05.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:05.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:05.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:05.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:05.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:05.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:05.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:05.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:05.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:05.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:05.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:05.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:05.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:05.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:05.364][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-26 18:17:05.364][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:05.365][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-26 18:17:05.365][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:05.365][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:05.366][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:05.366][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:05.366][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:05.366][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:05.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:05.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:05.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:05.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:05.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:05.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:05.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:05.371][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-26 18:17:05.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:05.372][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:05.372][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-26 18:17:05.710][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-26 18:17:06.415][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:06.416][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-26 18:17:06.418][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-26 18:17:06.419][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-26 18:17:06.419][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:06.419][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:06.420][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:06.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:06.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:06.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:06.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:06.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:06.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:06.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:06.430][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:06.430][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:06.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:06.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:06.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.432][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:06.433][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:06.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.433][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.433][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:06.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:06.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.435][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:06.435][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:06.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.436][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:06.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:06.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.437][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:06.437][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:06.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.437][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:06.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:06.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.439][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:06.439][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:06.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.440][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.440][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:06.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:06.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.441][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:06.441][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:06.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.442][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.442][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:06.442][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:06.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.443][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.443][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:06.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:06.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.444][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:06.444][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:06.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.445][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:06.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:06.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.446][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:06.446][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:06.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:06.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:06.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.448][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:06.449][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:06.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.449][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.449][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:06.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:06.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.450][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:06.451][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:06.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.451][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.452][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:06.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:06.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:06.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:06.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:06.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:06.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:06.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:06.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:06.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:06.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:06.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:06.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:06.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:06.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:06.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:06.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:06.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:06.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:06.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:06.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:06.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:06.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:06.466][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-26 18:17:06.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:06.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:06.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:06.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:06.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:06.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:06.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:06.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:06.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:06.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:06.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:06.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:06.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:06.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:06.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:06.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:06.473][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-26 18:17:06.473][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:06.474][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-26 18:17:06.474][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:06.474][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:06.475][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:06.475][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:06.475][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:06.475][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:06.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:06.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:06.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:06.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:06.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:06.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:06.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:06.480][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-26 18:17:06.481][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:06.481][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:06.481][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-26 18:17:06.833][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-26 18:17:07.195][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:07.200][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-26 18:17:07.202][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-26 18:17:07.203][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-26 18:17:07.204][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:07.204][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:07.204][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:07.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:07.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:07.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:07.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:07.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:07.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:07.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:07.209][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.209][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.211][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:07.212][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:07.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.212][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.213][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:07.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:07.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.214][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:07.214][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:07.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.215][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.215][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:07.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:07.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.216][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:07.216][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:07.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.217][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:07.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:07.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.218][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:07.219][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:07.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.219][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:07.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:07.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.220][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:07.221][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:07.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.221][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.222][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:07.222][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.222][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.223][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:07.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.224][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:07.224][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:07.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:07.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:07.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.226][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:07.226][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:07.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.227][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:07.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:07.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.228][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:07.229][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:07.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.229][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.232][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:07.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:07.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.234][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:07.234][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:07.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.235][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.235][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:07.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:07.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:07.246][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-26 18:17:07.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:07.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:07.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:07.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:07.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:07.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:07.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:07.253][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[2025-03-26 18:17:07.253][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-26 18:17:07.253][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:07.254][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-26 18:17:07.254][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:07.254][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:07.255][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:07.255][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:07.255][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:07.255][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:07.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:07.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:07.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:07.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:07.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:07.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:07.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:07.262][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-26 18:17:07.264][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:07.264][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:07.264][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-26 18:17:07.609][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-26 18:17:07.942][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:07.943][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-26 18:17:07.945][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-26 18:17:07.946][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-26 18:17:07.946][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:07.946][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:07.947][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:07.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:07.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:07.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:07.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:07.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:07.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:07.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:07.952][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.952][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.953][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.954][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:07.955][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:07.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.955][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.956][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:07.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:07.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.957][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:07.957][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:07.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.958][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.958][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:07.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:07.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.959][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:07.959][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:07.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.960][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:07.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:07.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.961][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:07.962][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:07.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.962][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:07.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:07.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.964][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:07.964][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:07.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.964][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.965][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:07.965][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.965][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.966][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:07.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.967][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:07.967][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:07.967][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.968][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:07.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:07.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.973][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:07.974][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:07.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:07.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:07.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.977][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:07.977][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:07.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.977][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.978][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:07.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:07.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.979][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:07.979][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:07.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.980][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.980][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:07.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:07.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:07.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:07.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:07.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:07.991][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-26 18:17:07.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:07.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:07.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:07.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:07.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:07.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:07.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:07.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:07.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:07.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:07.998][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[2025-03-26 18:17:07.998][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-26 18:17:07.999][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:07.999][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-26 18:17:08.000][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:08.000][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:08.000][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:08.004][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:08.005][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:08.005][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:08.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:08.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:08.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:08.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:08.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:08.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:08.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:08.011][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-26 18:17:08.012][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:08.012][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:08.012][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-26 18:17:08.349][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-26 18:17:08.683][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:08.683][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-26 18:17:08.685][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-26 18:17:08.686][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-26 18:17:08.686][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:08.687][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:08.687][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:08.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:08.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:08.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:08.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:08.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:08.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:08.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:08.692][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:08.692][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:08.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.693][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:08.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:08.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.694][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:08.695][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:08.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.695][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.695][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:08.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:08.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.696][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:08.697][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:08.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.697][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.698][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:08.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:08.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.699][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:08.699][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:08.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.699][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:08.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:08.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.701][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:08.701][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:08.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:08.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:08.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.703][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:08.703][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:08.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.704][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.704][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:08.704][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:08.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.705][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.710][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:08.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:08.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.711][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:08.712][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:08.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.712][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:08.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:08.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.714][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:08.714][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:08.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.714][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:08.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:08.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.716][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:08.716][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:08.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.717][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:08.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:08.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.718][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:08.719][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:08.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.719][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.719][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:08.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:08.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:08.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:08.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:08.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:08.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:08.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:08.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:08.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:08.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:08.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:08.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:08.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:08.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:08.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:08.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:08.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:08.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:08.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:08.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:08.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:08.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:08.731][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-26 18:17:08.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:08.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:08.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:08.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:08.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:08.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:08.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:08.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:08.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:08.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:08.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:08.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:08.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:08.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:08.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:08.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:08.742][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-26 18:17:08.742][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:08.742][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-26 18:17:08.743][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:08.743][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:08.743][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:08.744][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:08.744][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:08.744][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:08.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:08.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:08.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:08.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:08.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:08.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:08.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:08.749][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-26 18:17:08.750][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:08.750][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:08.750][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-26 18:17:09.092][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-26 18:17:09.436][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:09.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-26 18:17:09.439][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-26 18:17:09.440][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-26 18:17:09.440][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:09.441][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:09.441][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:09.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:09.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:09.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:09.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:09.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:09.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:09.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:09.446][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:09.446][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:09.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:09.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:09.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.448][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:09.449][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:09.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.449][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.450][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:09.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:09.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.451][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:09.451][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:09.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.452][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.452][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:09.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:09.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.453][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:09.453][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:09.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.454][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:09.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:09.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.455][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:09.456][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:09.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.460][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.461][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:09.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:09.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.462][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:09.463][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:09.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.463][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.463][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:09.464][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:09.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.464][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:09.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:09.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.466][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:09.466][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:09.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.466][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:09.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:09.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.468][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:09.468][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:09.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.469][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:09.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:09.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.470][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:09.470][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:09.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.471][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.471][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:09.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:09.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.472][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:09.472][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:09.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.473][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:09.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:09.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:09.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:09.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:09.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:09.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:09.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:09.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:09.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:09.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:09.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:09.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:09.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:09.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:09.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:09.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:09.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:09.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:09.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:09.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:09.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:09.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:09.484][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-26 18:17:09.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:09.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:09.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:09.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:09.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:09.491][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:09.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:09.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:09.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:09.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:09.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:09.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:09.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:09.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:09.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:09.495][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[2025-03-26 18:17:09.495][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-26 18:17:09.495][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:09.496][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-26 18:17:09.496][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:09.497][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:09.497][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:09.497][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:09.497][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:09.498][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:09.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:09.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:09.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:09.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:09.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:09.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:09.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:09.502][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-26 18:17:09.503][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:09.503][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:09.503][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-26 18:17:09.868][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-26 18:17:10.197][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:10.198][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-26 18:17:10.200][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-26 18:17:10.200][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-26 18:17:10.201][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:10.201][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:10.202][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:10.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:10.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:10.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:10.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:10.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:10.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:10.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:10.207][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:10.207][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:10.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.208][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:10.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:10.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.209][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:10.210][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:10.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.211][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:10.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:10.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.212][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:10.212][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:10.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.213][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.213][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:10.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:10.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.221][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:10.222][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:10.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.222][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:10.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:10.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.224][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:10.224][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:10.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.225][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:10.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:10.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.226][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:10.227][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:10.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.227][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.228][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:10.228][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:10.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.229][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.229][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:10.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:10.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.230][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:10.231][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:10.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:10.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:10.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.233][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:10.233][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:10.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.234][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:10.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:10.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.235][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:10.236][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:10.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.236][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.237][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:10.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:10.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.238][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:10.238][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:10.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.239][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.239][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:10.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:10.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:10.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:10.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:10.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:10.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:10.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:10.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:10.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:10.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:10.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:10.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:10.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:10.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:10.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:10.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:10.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:10.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:10.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:10.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:10.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:10.256][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-26 18:17:10.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:10.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:10.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:10.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:10.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:10.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:10.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:10.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:10.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:10.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:10.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:10.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:10.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:10.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:10.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:10.263][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[2025-03-26 18:17:10.264][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-26 18:17:10.264][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:10.264][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-26 18:17:10.265][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:10.265][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:10.265][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:10.266][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:10.266][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:10.266][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:10.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:10.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:10.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:10.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:10.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:10.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:10.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:10.270][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-26 18:17:10.271][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:10.271][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:10.272][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-26 18:17:10.842][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-26 18:17:11.171][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:11.172][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-26 18:17:11.173][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-26 18:17:11.174][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-26 18:17:11.175][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:11.175][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:11.175][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:11.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:11.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:11.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:11.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:11.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:11.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:11.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:11.180][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:11.180][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:11.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.181][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:11.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:11.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.187][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:11.187][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:11.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.188][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.188][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:11.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:11.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.189][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:11.190][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:11.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.190][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.191][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:11.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:11.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.192][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:11.192][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:11.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.192][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:11.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:11.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.194][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:11.194][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:11.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.195][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:11.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:11.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.196][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:11.196][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:11.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.197][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.197][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:11.197][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:11.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.198][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.198][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:11.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:11.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.199][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:11.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:11.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.200][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:11.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:11.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.201][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:11.201][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:11.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.202][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:11.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:11.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.203][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:11.203][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:11.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.204][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.204][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:11.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:11.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.205][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:11.205][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:11.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.206][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.206][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:11.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:11.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:11.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:11.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:11.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:11.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:11.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:11.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:11.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:11.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:11.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:11.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:11.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:11.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:11.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:11.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:11.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:11.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:11.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:11.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:11.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:11.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:11.223][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-26 18:17:11.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:11.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:11.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:11.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:11.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:11.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:11.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:11.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:11.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:11.234][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:11.235][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:11.235][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:11.236][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:11.652][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:12.053][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:12.053][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-26 18:17:12.055][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-26 18:17:12.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.077][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:12.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:12.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:12.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:12.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:12.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:12.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:12.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:12.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:12.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:12.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:12.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:12.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:12.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:12.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:12.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:12.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:12.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:12.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:12.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:12.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:12.315][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:12.316][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:12.317][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:12.317][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:12.647][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:12.994][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:12.995][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-26 18:17:12.996][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-26 18:17:12.997][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:12.998][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:12.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:12.999][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:13.327][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:13.655][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:13.662][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-26 18:17:13.663][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-26 18:17:13.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:13.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:13.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:13.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:13.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:13.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:13.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:13.668][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-26 18:17:13.668][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:13.668][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-26 18:17:13.669][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:13.669][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:13.669][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:13.669][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:13.670][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:13.670][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:13.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:13.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:13.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:13.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:13.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:13.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:13.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:13.674][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-26 18:17:13.675][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:13.675][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:13.675][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-26 18:17:14.015][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-26 18:17:14.592][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:14.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-26 18:17:14.594][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-26 18:17:14.595][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-26 18:17:14.596][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:14.596][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:14.597][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:14.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:14.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:14.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:14.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:14.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:14.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:14.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:14.601][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:14.601][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:14.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.602][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:14.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:14.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.603][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:14.604][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:14.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.604][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.604][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:14.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:14.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.606][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:14.606][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:14.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.606][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.607][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:14.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:14.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.608][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:14.608][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:14.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.608][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:14.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:14.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.610][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:14.610][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:14.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.611][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:14.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:14.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.612][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:14.612][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:14.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.613][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.613][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:14.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:14.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.614][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:14.614][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:14.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.615][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.615][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:14.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:14.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.616][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.617][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.617][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.619][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:14.619][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:14.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.619][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:14.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:14.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.621][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:14.622][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:14.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.622][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.623][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:14.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:14.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.624][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:14.624][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:14.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.625][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:14.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:14.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:14.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:14.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:14.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:14.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:14.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:14.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:14.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:14.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:14.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:14.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:14.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:14.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:14.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:14.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:14.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:14.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:14.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:14.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:14.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:14.638][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-26 18:17:14.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:14.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:14.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:14.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:14.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:14.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:14.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:14.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:14.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:14.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:14.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:14.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:14.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:14.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:14.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:14.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:14.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:14.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:14.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:14.653][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-26 18:17:14.653][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:14.653][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-26 18:17:14.654][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:14.654][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:14.654][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:14.655][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:14.655][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:14.655][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:14.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:14.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:14.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:14.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:14.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:14.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:14.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:14.660][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-26 18:17:14.661][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:14.661][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:14.662][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-26 18:17:15.207][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-26 18:17:15.545][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:15.546][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-26 18:17:15.547][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-26 18:17:15.548][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-26 18:17:15.549][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:15.549][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:15.549][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:15.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.554][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[2025-03-26 18:17:15.555][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:15.555][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:15.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.555][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:15.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:15.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.557][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:15.558][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:15.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.558][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.559][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:15.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:15.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.560][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:15.560][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:15.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:15.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:15.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.562][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:15.562][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:15.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.563][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:15.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:15.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.564][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:15.565][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:15.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.565][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:15.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:15.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.566][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:15.567][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:15.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.567][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.568][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:15.568][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:15.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.569][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:15.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:15.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.570][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.573][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.577][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:15.577][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:15.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:15.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:15.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.579][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:15.579][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:15.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.580][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.580][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:15.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:15.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.581][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:15.581][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:15.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.582][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.582][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:15.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:15.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:15.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:15.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:15.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:15.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:15.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:15.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:15.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:15.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:15.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:15.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:15.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:15.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:15.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:15.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:15.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:15.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:15.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:15.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:15.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:15.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.593][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-26 18:17:15.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.604][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:15.605][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:15.605][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 18:17:15.606][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:15.606][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-26 18:17:15.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.751][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:15.752][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:15.753][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 18:17:15.753][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:15.754][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-26 18:17:15.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.791][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:15.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:15.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.896][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-26 18:17:15.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-26 18:17:15.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 18:17:15.900][biodb::testThat]
biodb.INFO [2025-03-26 18:17:15.900][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-26 18:17:15.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:15.900][biodb::testThat]
biodb.TRACE[2025-03-26 18:17:15.901][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 18:17:15.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 18:17:15.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:15.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:15.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:15.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:15.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:15.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:15.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:15.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:15.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:15.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:15.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:15.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:15.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:15.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:15.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:15.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:15.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:15.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:15.911][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:15.912][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:15.912][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:15.913][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:16.240][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:16.569][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:16.570][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-26 18:17:16.571][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-26 18:17:16.573][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:16.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:16.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:16.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:16.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:16.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:16.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:16.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:16.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:16.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:16.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:16.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:16.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:16.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:16.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:16.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:16.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:16.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:16.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:16.580][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:16.581][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:16.581][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:16.582][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:16.911][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:17.239][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:17.240][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-26 18:17:17.241][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-26 18:17:17.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:17.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:17.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:17.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:17.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:17.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:17.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:17.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:17.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:17.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:17.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:17.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:17.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:17.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:17.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:17.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:17.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:17.257][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 18:17:17.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:17.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:17.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:17.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:17.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:17.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:17.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:17.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.264][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.264][private$selectFields]
biodb.TRACE[2025-03-26 18:17:17.264][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:17.265][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:17.265][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.265][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.266][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.266][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.266][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.267][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.267][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.267][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.267][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.268][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.268][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.269][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:17.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.275][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-26 18:17:17.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:17.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:17.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:17.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:17.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:17.279][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:17.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:17.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.282][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.282][private$selectFields]
biodb.TRACE[2025-03-26 18:17:17.283][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:17.283][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:17.283][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.283][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.284][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.284][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.284][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.285][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.285][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.286][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.286][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.286][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.287][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:17.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.290][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 18:17:17.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:17.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:17.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:17.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:17.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:17.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:17.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:17.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.296][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.296][private$selectFields]
biodb.TRACE[2025-03-26 18:17:17.297][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:17.297][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:17.297][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.297][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.298][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.298][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.298][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.299][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.299][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.299][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.300][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:17.300][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.300][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.301][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.301][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:17.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:17.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.304][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-26 18:17:17.305][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 18:17:17.305][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 18:17:17.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:17.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:17.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:17.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:17.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:17.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:17.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:17.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:17.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:17.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:17.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:17.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:17.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:17.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:17.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:17.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:17.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:17.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:17.342][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:17.343][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:17.343][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:17.344][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:17.674][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:18.001][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:18.002][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-26 18:17:18.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-26 18:17:18.005][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:18.006][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:18.006][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:18.007][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:18.545][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:19.143][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:19.144][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-26 18:17:19.146][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-26 18:17:19.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.173][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 18:17:19.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.185][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.185][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.186][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.186][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.186][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.186][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.187][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.187][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.188][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.188][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.188][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.188][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.189][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.189][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.189][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.190][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.193][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-26 18:17:19.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.213][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.213][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.213][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.213][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.214][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.214][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.214][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.215][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.215][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.215][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.216][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.216][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.219][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.219][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.219][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.220][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.223][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 18:17:19.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.229][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.229][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.230][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.230][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.230][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.230][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.231][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.231][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.232][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.232][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.232][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.233][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.233][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.234][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.237][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-26 18:17:19.237][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 18:17:19.237][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 18:17:19.240][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-26 18:17:19.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-26 18:17:19.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 18:17:19.242][biodb::testThat]
biodb.INFO [2025-03-26 18:17:19.243][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-26 18:17:19.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:19.243][biodb::testThat]
biodb.TRACE[2025-03-26 18:17:19.244][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 18:17:19.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 18:17:19.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:19.253][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:19.254][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:19.255][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-26 18:17:19.255][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:19.256][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-26 18:17:19.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.262][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:19.263][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:19.264][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-26 18:17:19.264][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:19.264][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-26 18:17:19.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.271][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.272][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.279][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 18:17:19.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.285][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.285][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.286][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.286][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.286][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.286][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.287][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.287][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.288][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.288][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.288][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.289][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.289][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.289][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.290][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.294][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-26 18:17:19.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.300][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.301][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.301][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.301][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.301][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.302][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.302][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.303][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.303][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.303][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.304][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.304][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.304][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.305][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.305][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.305][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.312][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 18:17:19.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.318][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.319][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.319][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.319][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.319][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.320][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.320][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.321][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.321][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.321][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.322][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.322][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.322][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.322][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.323][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.323][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.323][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.327][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-26 18:17:19.327][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 18:17:19.327][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 18:17:19.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:19.339][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:19.341][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:19.341][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-26 18:17:19.341][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:19.342][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-26 18:17:19.343][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:19.344][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:19.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-26 18:17:19.345][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:19.345][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-26 18:17:19.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.365][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 18:17:19.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.370][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.371][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.371][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.371][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.371][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.372][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.372][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.372][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.373][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.373][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.373][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.374][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.374][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.374][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.374][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.375][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.375][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.379][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-26 18:17:19.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.384][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.384][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.385][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.385][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.385][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.385][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.386][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.386][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.386][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.387][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.387][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.387][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.388][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.388][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.389][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.389][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.392][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 18:17:19.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.398][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.398][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.398][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.399][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.399][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.399][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.399][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.400][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.400][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.400][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.401][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.401][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.401][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.402][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.403][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.406][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-26 18:17:19.406][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 18:17:19.407][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 18:17:19.412][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-26 18:17:19.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-26 18:17:19.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 18:17:19.415][biodb::testThat]
biodb.INFO [2025-03-26 18:17:19.415][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-26 18:17:19.415][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:19.416][biodb::testThat]
biodb.TRACE[2025-03-26 18:17:19.417][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 18:17:19.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 18:17:19.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:19.427][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:19.428][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:19.428][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-26 18:17:19.429][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:19.429][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-26 18:17:19.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.436][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:19.437][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:19.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-26 18:17:19.437][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:19.438][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-26 18:17:19.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:19.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.451][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 18:17:19.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.456][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.457][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.457][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.457][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.457][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.458][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.458][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.458][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.459][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.459][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.459][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.460][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.460][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.460][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.460][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.461][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.461][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.465][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-26 18:17:19.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.470][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.470][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.471][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.471][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.471][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.471][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.472][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.472][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.472][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.473][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.473][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.474][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.474][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.474][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.475][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.475][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.478][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 18:17:19.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.484][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.484][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.485][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.485][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.485][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.485][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.486][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.486][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.486][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.486][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.487][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.487][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.487][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.488][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.488][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.488][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.489][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.492][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-26 18:17:19.492][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 18:17:19.493][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 18:17:19.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:19.509][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:19.510][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:19.510][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-26 18:17:19.511][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:19.511][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-26 18:17:19.513][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:19.517][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:19.517][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-26 18:17:19.518][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:19.518][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-26 18:17:19.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:19.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:19.538][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 18:17:19.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.544][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.544][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.544][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.544][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.545][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.545][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.545][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.546][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.546][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.547][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.547][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.547][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.548][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.548][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.548][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.549][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.552][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-26 18:17:19.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.558][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.559][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.559][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.559][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.559][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.560][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.560][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.560][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.561][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.561][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.562][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.562][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.562][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.562][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.563][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.563][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.567][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 18:17:19.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:19.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.573][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.573][private$selectFields]
biodb.TRACE[2025-03-26 18:17:19.573][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 18:17:19.574][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 18:17:19.574][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.574][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.574][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.575][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.575][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.575][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.576][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.576][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 18:17:19.577][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.577][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.577][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.578][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 18:17:19.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:19.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:19.581][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-26 18:17:19.581][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 18:17:19.582][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 18:17:19.588][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-26 18:17:19.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-26 18:17:19.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:19.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 18:17:19.591][biodb::testThat]
biodb.INFO [2025-03-26 18:17:19.591][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-03-26 18:17:19.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:19.591][biodb::testThat]
biodb.DEBUG[2025-03-26 18:17:19.592][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-26 18:17:19.592][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:19.593][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-26 18:17:19.593][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:19.593][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:19.594][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:19.594][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:19.594][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:19.594][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:19.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:19.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:19.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:19.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:19.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:19.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:19.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:19.599][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-26 18:17:19.600][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:19.600][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:19.600][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-26 18:17:26.276][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-26 18:17:26.633][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:26.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-26 18:17:26.635][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-26 18:17:26.636][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-26 18:17:26.636][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:26.636][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:26.637][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:26.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:26.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:26.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:26.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:26.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:26.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:26.640][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.TRACE[2025-03-26 18:17:26.641][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:26.641][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:26.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.642][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:26.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:26.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.643][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:26.644][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:26.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.644][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.645][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:26.645][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:26.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.645][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.646][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:26.646][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:26.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.646][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.647][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:26.647][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:26.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.647][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.648][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:26.648][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:26.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.649][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.649][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:26.649][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:26.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.650][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.650][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:26.650][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:26.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.655][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.655][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:26.656][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:26.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.656][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.656][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:26.657][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:26.657][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.658][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:26.658][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:26.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.658][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:26.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:26.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:26.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:26.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:26.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:26.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:26.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:26.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:26.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:26.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:26.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:26.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:26.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:26.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:26.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:26.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:26.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:26.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:26.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:26.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:26.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:26.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:26.669][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-26 18:17:26.670][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-26 18:17:26.672][biodb::testThat]
biodb.INFO [2025-03-26 18:17:26.673][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-26 18:17:26.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:26.673][biodb::testThat]
biodb.DEBUG[2025-03-26 18:17:26.676][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-26 18:17:26.677][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-26 18:17:26.677][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-26 18:17:26.678][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-26 18:17:26.678][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-26 18:17:26.678][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:26.679][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:26.679][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:26.679][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:26.679][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:26.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:26.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:26.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:26.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:26.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:26.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:26.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:26.684][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-26 18:17:26.684][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:26.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:26.685][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-26 18:17:27.413][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-26 18:17:27.743][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:27.744][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-26 18:17:27.745][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-26 18:17:27.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:27.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:27.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:27.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:27.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:27.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:27.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:27.750][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-03-26 18:17:27.750][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:27.751][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:27.751][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-26 18:17:28.080][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-26 18:17:28.415][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:28.416][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-26 18:17:28.417][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-26 18:17:28.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:28.418][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:28.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:28.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:28.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:28.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:28.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:28.421][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-26 18:17:28.422][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:28.423][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:28.423][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-26 18:17:28.753][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-26 18:17:29.089][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:29.089][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-26 18:17:29.090][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-26 18:17:29.091][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-26 18:17:29.092][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:29.092][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-26 18:17:29.093][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:29.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:29.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:29.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:29.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:29.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:29.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:29.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:29.097][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.097][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.098][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.099][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:29.099][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:29.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.100][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.100][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:29.100][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:29.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.101][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.101][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:29.101][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:29.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.102][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.102][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:29.102][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:29.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.103][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:29.103][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:29.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.104][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.104][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:29.104][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:29.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.105][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.105][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:29.105][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:29.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.106][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:29.106][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:29.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.107][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.107][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:29.107][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:29.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.108][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.108][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:29.108][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:29.109][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:29.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:29.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:29.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:29.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:29.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:29.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:29.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:29.119][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.119][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.120][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.121][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:29.121][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:29.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.122][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.122][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:29.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:29.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.123][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:29.123][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:29.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.124][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.124][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:29.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:29.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.125][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:29.125][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:29.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.126][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:29.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:29.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.127][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:29.127][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:29.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.128][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:29.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:29.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.129][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:29.129][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:29.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.130][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:29.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:29.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.131][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:29.131][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:29.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.132][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.132][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:29.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:29.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.133][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:29.133][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:29.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.134][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:29.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.135][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:29.135][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:29.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.136][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:29.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:29.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.137][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:29.137][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:29.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.138][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:29.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:29.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.144][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:29.144][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:29.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.144][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.145][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:29.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:29.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:29.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:29.152][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:29.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:29.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:29.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:29.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:29.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:29.156][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.156][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.157][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.158][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:29.158][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:29.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.158][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.159][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:29.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:29.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.160][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:29.160][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:29.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.160][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.161][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:29.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:29.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.162][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:29.162][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:29.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.162][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:29.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:29.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.163][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:29.164][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:29.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.164][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:29.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.165][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:29.166][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:29.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.166][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:29.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:29.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.167][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:29.168][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:29.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.168][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.168][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:29.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:29.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.169][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:29.170][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:29.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.170][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:29.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:29.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.171][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:29.172][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:29.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:29.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:29.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.173][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:29.174][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:29.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.174][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.174][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:29.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:29.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.175][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:29.176][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:29.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.176][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.176][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:29.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:29.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:29.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:29.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:29.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:29.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:29.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:29.192][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-26 18:17:29.192][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-26 18:17:29.193][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-26 18:17:29.197][biodb::testThat]
biodb.INFO [2025-03-26 18:17:29.197][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-03-26 18:17:29.198][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:29.198][biodb::testThat]
biodb.INFO [2025-03-26 18:17:29.205][biodb::testThat]
biodb.INFO [2025-03-26 18:17:29.206][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-03-26 18:17:29.206][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:29.206][biodb::testThat]
biodb.INFO [2025-03-26 18:17:29.208][biodb::testThat]
biodb.INFO [2025-03-26 18:17:29.209][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-03-26 18:17:29.209][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:29.209][biodb::testThat]
biodb.DEBUG[2025-03-26 18:17:29.210][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:29.211][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:29.211][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:29.212][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:29.578][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:30.049][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:30.050][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-26 18:17:30.051][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-26 18:17:30.055][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:30.056][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:30.056][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:30.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:30.057][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:30.057][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:30.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:30.057][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 18:17:30.058][biodb::testThat]
biodb.INFO [2025-03-26 18:17:30.058][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-26 18:17:30.058][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:30.059][biodb::testThat]
biodb.ERROR[2025-03-26 18:17:30.063][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-26 18:17:30.069][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-26 18:17:30.073][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 18:17:30.073][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-26 18:17:30.074][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-26 18:17:30.074][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 18:17:30.078][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.078][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.079][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.079][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.INFO [2025-03-26 18:17:30.082][biodb::testContext]
biodb.INFO [2025-03-26 18:17:30.083][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 18:17:30.083][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-26 18:17:30.083][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 18:17:30.083][biodb::testContext]
biodb.INFO [2025-03-26 18:17:30.084][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 18:17:30.085][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 18:17:30.086][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:17:30.087][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 18:17:30.087][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 18:17:30.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.088][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 18:17:30.088][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 18:17:30.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.089][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 18:17:30.089][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 18:17:30.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.090][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 18:17:30.091][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 18:17:30.091][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 18:17:30.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.092][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 18:17:30.092][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 18:17:30.092][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 18:17:30.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.093][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 18:17:30.093][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 18:17:30.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.094][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 18:17:30.095][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 18:17:30.095][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 18:17:30.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.096][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 18:17:30.096][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 18:17:30.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.097][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 18:17:30.097][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 18:17:30.097][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 18:17:30.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.098][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 18:17:30.098][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 18:17:30.099][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 18:17:30.099][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 18:17:30.099][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 18:17:30.099][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 18:17:30.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.100][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 18:17:30.101][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 18:17:30.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.101][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 18:17:30.102][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 18:17:30.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.103][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 18:17:30.103][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 18:17:30.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.104][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 18:17:30.104][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 18:17:30.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.105][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 18:17:30.105][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 18:17:30.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.106][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 18:17:30.106][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 18:17:30.112][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 18:17:30.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.113][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 18:17:30.113][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 18:17:30.113][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 18:17:30.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.114][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 18:17:30.115][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.115][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-26 18:17:30.115][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.116][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:30.116][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.116][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.116][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.117][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.117][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 18:17:30.117][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:30.117][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.118][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 18:17:30.118][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:30.118][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.118][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.119][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:17:30.119][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:17:30.119][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:17:30.119][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 18:17:30.119][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 18:17:30.119][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:30.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:30.119][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:30.120][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:30.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:30.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:30.120][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.121][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.121][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:30.121][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:30.121][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.122][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.122][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 18:17:30.122][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.123][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 18:17:30.123][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.123][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:30.123][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.124][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.124][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.124][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.124][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 18:17:30.125][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:30.125][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.125][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 18:17:30.125][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:30.126][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.126][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.126][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:17:30.126][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:17:30.126][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:17:30.126][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 18:17:30.126][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 18:17:30.126][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:30.127][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:30.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:30.127][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:30.127][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:30.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:30.128][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.128][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.128][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:30.129][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:30.129][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.129][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.129][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 18:17:30.130][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.130][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-26 18:17:30.130][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.131][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:30.131][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.131][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.131][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.132][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.132][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 18:17:30.132][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:30.132][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.133][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 18:17:30.133][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:30.133][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.133][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.134][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.134][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:30.134][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:30.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:30.135][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:30.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:30.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:30.135][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.136][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.136][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:30.136][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:30.136][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.137][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.137][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 18:17:30.137][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.138][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 18:17:30.138][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.138][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:30.139][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.139][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.139][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.139][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.140][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 18:17:30.140][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:30.140][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.140][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 18:17:30.141][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:30.141][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.141][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.141][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.142][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:30.142][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:30.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:30.142][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:30.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:30.143][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:30.143][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.143][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.144][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:30.144][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:30.144][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.144][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:30.145][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:17:30.145][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.156][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[2025-03-26 18:17:30.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.158][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[2025-03-26 18:17:30.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.162][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.DEBUG[2025-03-26 18:17:30.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.163][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[2025-03-26 18:17:30.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.165][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 18:17:30.165][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 18:17:30.166][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 18:17:30.166][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 18:17:30.166][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 18:17:30.167][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 18:17:30.167][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 18:17:30.167][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 18:17:30.168][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 18:17:30.168][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 18:17:30.169][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 18:17:30.169][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 18:17:30.169][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 18:17:30.170][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 18:17:30.170][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 18:17:30.170][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 18:17:30.171][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 18:17:30.171][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 18:17:30.174][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 18:17:30.174][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 18:17:30.175][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 18:17:30.175][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 18:17:30.176][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 18:17:30.176][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 18:17:30.176][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 18:17:30.177][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 18:17:30.177][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 18:17:30.177][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 18:17:30.178][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 18:17:30.178][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 18:17:30.178][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 18:17:30.179][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 18:17:30.179][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 18:17:30.179][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 18:17:30.180][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 18:17:30.180][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 18:17:30.181][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 18:17:30.181][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 18:17:30.181][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 18:17:30.182][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 18:17:30.182][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 18:17:30.182][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 18:17:30.183][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 18:17:30.183][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 18:17:30.183][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 18:17:30.184][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 18:17:30.184][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 18:17:30.185][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 18:17:30.185][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 18:17:30.185][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 18:17:30.186][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 18:17:30.186][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 18:17:30.186][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 18:17:30.187][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 18:17:30.187][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 18:17:30.187][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 18:17:30.188][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 18:17:30.188][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 18:17:30.188][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 18:17:30.189][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 18:17:30.189][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 18:17:30.190][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 18:17:30.190][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 18:17:30.190][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 18:17:30.191][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 18:17:30.191][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 18:17:30.191][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 18:17:30.192][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 18:17:30.192][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 18:17:30.192][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 18:17:30.193][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 18:17:30.193][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 18:17:30.194][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 18:17:30.194][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 18:17:30.194][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 18:17:30.195][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 18:17:30.195][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 18:17:30.195][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 18:17:30.196][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 18:17:30.196][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 18:17:30.196][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 18:17:30.197][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 18:17:30.197][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 18:17:30.198][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 18:17:30.198][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 18:17:30.198][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:17:30.199][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.199][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.217][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.DEBUG[2025-03-26 18:17:30.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:30.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:30.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:30.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:30.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:30.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:30.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:30.228][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-26 18:17:30.228][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-26 18:17:30.229][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.229][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.230][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.230][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:30.230][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.230][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.231][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.231][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-26 18:17:30.231][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 18:17:30.231][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-26 18:17:30.232][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-26 18:17:30.233][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:30.233][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:17:30.233][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:17:30.233][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:17:30.233][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 18:17:30.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:30.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:30.234][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:30.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:30.234][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:30.235][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:30.235][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:30.235][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-26 18:17:30.235][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:30.235][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:30.235][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:30.236][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-26 18:17:30.236][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-26 18:17:30.238][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 18:17:30.238][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 18:17:30.239][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-26 18:17:30.239][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 18:17:30.239][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 18:17:30.240][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 18:17:30.241][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-26 18:17:30.241][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-26 18:17:30.241][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-26 18:17:30.242][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-26 18:17:30.242][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 18:17:30.242][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 18:17:30.243][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-26 18:17:30.243][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-26 18:17:30.243][biodb::testThat]
biodb.INFO [2025-03-26 18:17:30.244][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-03-26 18:17:30.244][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:30.244][biodb::testThat]
biodb.DEBUG[2025-03-26 18:17:30.245][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-26 18:17:30.246][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:30.247][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:30.247][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-26 18:17:30.572][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-26 18:17:31.056][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:31.056][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-26 18:17:31.058][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-26 18:17:31.059][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:31.060][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:31.060][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:31.065][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:31.392][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:31.719][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:31.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-26 18:17:31.721][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-26 18:17:31.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:31.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:31.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:31.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:31.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:31.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:31.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:31.726][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:31.733][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:31.734][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:31.734][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:32.062][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:32.390][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:32.391][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-26 18:17:32.392][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-26 18:17:32.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:32.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:32.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:32.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:32.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:32.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:32.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:32.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:32.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:32.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:32.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:32.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:32.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:32.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:32.407][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:32.408][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:32.409][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-26 18:17:32.409][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:32.410][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-26 18:17:32.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:32.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:32.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:32.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:32.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:32.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:32.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:32.414][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:32.415][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:32.416][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-26 18:17:32.416][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:32.416][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-26 18:17:32.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:32.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:32.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:32.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:32.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:32.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:32.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:32.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:32.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:32.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:32.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:32.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:32.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:32.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:32.424][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:32.425][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:32.425][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-26 18:17:32.426][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:32.426][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-26 18:17:32.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:32.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:32.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:32.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:32.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:32.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:32.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:32.430][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:32.431][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:32.431][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-26 18:17:32.432][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:32.432][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-26 18:17:32.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:32.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:32.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:32.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:32.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:32.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:32.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:32.436][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:32.437][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:32.437][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:32.437][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:33.123][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:33.491][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:33.492][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-26 18:17:33.493][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-26 18:17:33.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:33.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:33.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:33.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:33.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:33.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:33.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-26 18:17:33.499][biodb::testThat]
biodb.INFO [2025-03-26 18:17:33.500][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-03-26 18:17:33.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:33.500][biodb::testThat]
biodb.DEBUG[2025-03-26 18:17:33.501][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:33.502][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:33.502][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:33.503][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:33.882][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:35.201][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:35.202][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-26 18:17:35.203][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-26 18:17:35.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:35.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:35.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:35.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.209][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:35.210][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:35.211][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:35.211][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:35.548][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:35.875][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:35.876][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-26 18:17:35.877][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-26 18:17:35.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:35.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:35.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:35.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-26 18:17:35.882][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 18:17:35.882][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-26 18:17:35.883][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-26 18:17:35.883][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 18:17:35.883][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:35.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:35.884][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.884][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.884][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.INFO [2025-03-26 18:17:35.885][biodb::testContext]
biodb.INFO [2025-03-26 18:17:35.886][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 18:17:35.886][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-26 18:17:35.886][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 18:17:35.886][biodb::testContext]
biodb.INFO [2025-03-26 18:17:35.887][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 18:17:35.887][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 18:17:35.889][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:17:35.889][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 18:17:35.889][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 18:17:35.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.890][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 18:17:35.891][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 18:17:35.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.891][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[2025-03-26 18:17:35.891][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 18:17:35.892][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 18:17:35.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.893][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 18:17:35.893][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 18:17:35.893][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 18:17:35.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.894][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 18:17:35.894][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 18:17:35.894][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 18:17:35.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.895][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 18:17:35.895][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 18:17:35.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.896][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 18:17:35.896][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 18:17:35.897][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 18:17:35.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.898][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 18:17:35.898][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 18:17:35.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.899][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 18:17:35.899][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 18:17:35.899][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 18:17:35.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.900][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 18:17:35.900][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 18:17:35.900][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 18:17:35.901][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 18:17:35.901][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 18:17:35.901][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 18:17:35.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.902][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 18:17:35.902][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 18:17:35.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.903][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 18:17:35.903][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 18:17:35.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.904][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 18:17:35.904][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 18:17:35.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.905][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 18:17:35.905][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 18:17:35.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.906][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[2025-03-26 18:17:35.906][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 18:17:35.907][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 18:17:35.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.913][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 18:17:35.913][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 18:17:35.919][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 18:17:35.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.920][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[2025-03-26 18:17:35.920][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 18:17:35.920][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 18:17:35.921][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 18:17:35.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.922][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 18:17:35.922][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.923][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-26 18:17:35.923][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.923][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:35.923][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.924][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.924][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.924][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 18:17:35.925][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:35.925][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.925][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 18:17:35.925][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:35.926][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.926][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.926][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:17:35.926][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:17:35.926][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:17:35.926][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 18:17:35.926][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 18:17:35.926][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:35.927][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:35.927][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:35.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:35.927][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:35.928][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:35.928][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.928][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.928][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:35.928][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:35.929][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.929][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.929][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 18:17:35.930][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.930][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 18:17:35.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:35.931][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.931][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.931][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.932][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.932][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 18:17:35.932][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:35.932][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.933][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 18:17:35.933][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:35.933][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.933][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.934][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:17:35.934][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:17:35.934][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:17:35.934][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 18:17:35.934][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 18:17:35.934][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:35.934][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:35.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:35.935][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:35.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:35.935][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:35.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.936][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.936][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:35.936][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:35.936][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.936][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.937][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 18:17:35.937][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.938][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-26 18:17:35.938][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.938][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:35.938][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.939][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.939][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.940][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.940][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 18:17:35.940][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:35.941][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.941][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 18:17:35.941][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:35.941][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.942][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.942][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.942][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:35.942][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:35.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:35.943][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:35.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:35.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:35.944][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.944][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.944][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:35.944][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:35.945][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.945][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.945][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 18:17:35.946][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.946][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 18:17:35.946][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.946][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:35.947][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.947][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.947][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.948][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.948][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 18:17:35.948][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:35.948][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.949][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 18:17:35.949][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:35.949][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.949][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:35.950][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.950][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:35.950][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:35.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:35.951][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:35.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:35.951][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:35.951][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:35.952][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.952][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:35.952][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:35.952][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:35.952][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:35.953][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:17:35.953][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.954][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[2025-03-26 18:17:35.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.957][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[2025-03-26 18:17:35.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.959][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[2025-03-26 18:17:35.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.964][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[2025-03-26 18:17:35.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.969][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[2025-03-26 18:17:35.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.971][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[2025-03-26 18:17:35.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:35.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:35.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:35.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:35.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:35.973][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 18:17:35.973][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 18:17:35.974][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 18:17:35.974][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 18:17:35.975][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 18:17:35.975][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 18:17:35.975][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 18:17:35.976][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 18:17:35.976][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 18:17:35.976][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 18:17:35.977][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 18:17:35.977][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 18:17:35.978][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 18:17:35.978][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 18:17:35.978][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 18:17:35.979][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 18:17:35.979][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 18:17:35.979][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 18:17:35.980][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 18:17:35.980][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 18:17:35.980][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 18:17:35.981][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 18:17:35.981][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 18:17:35.982][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 18:17:35.982][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 18:17:35.982][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 18:17:35.983][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 18:17:35.983][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 18:17:35.983][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 18:17:35.984][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 18:17:35.984][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 18:17:35.984][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 18:17:35.985][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 18:17:35.985][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 18:17:35.986][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 18:17:35.986][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 18:17:35.986][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 18:17:35.987][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 18:17:35.987][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 18:17:35.987][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 18:17:35.988][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 18:17:35.988][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 18:17:35.989][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 18:17:35.989][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 18:17:35.989][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 18:17:35.990][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 18:17:35.990][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 18:17:35.990][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 18:17:35.991][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 18:17:35.991][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 18:17:35.991][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 18:17:35.992][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 18:17:35.992][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 18:17:35.993][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 18:17:35.993][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 18:17:35.993][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 18:17:35.994][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 18:17:35.994][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 18:17:35.994][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 18:17:35.995][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 18:17:35.995][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 18:17:35.996][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 18:17:35.996][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 18:17:35.996][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 18:17:35.997][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 18:17:35.997][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 18:17:35.998][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 18:17:35.998][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 18:17:35.998][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 18:17:35.999][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 18:17:35.999][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 18:17:35.999][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 18:17:36.000][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 18:17:36.000][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 18:17:36.000][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 18:17:36.001][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 18:17:36.001][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 18:17:36.001][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 18:17:36.002][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 18:17:36.002][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 18:17:36.003][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 18:17:36.003][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 18:17:36.003][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 18:17:36.004][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 18:17:36.004][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 18:17:36.005][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:17:36.005][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.005][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.012][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[2025-03-26 18:17:36.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.017][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[2025-03-26 18:17:36.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.020][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[2025-03-26 18:17:36.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.022][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[2025-03-26 18:17:36.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.037][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-26 18:17:36.037][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-26 18:17:36.038][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.038][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.039][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.039][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:36.039][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.039][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.040][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.040][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-26 18:17:36.040][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 18:17:36.041][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:36.041][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.041][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:17:36.042][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:17:36.043][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 18:17:36.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.043][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:36.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.044][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.044][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:36.044][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-26 18:17:36.045][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:36.045][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:36.045][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.045][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-26 18:17:36.045][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-26 18:17:36.048][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 18:17:36.048][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 18:17:36.049][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-26 18:17:36.049][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 18:17:36.049][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 18:17:36.050][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 18:17:36.051][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-26 18:17:36.051][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-26 18:17:36.051][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-26 18:17:36.052][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-26 18:17:36.052][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 18:17:36.053][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 18:17:36.053][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-26 18:17:36.053][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-26 18:17:36.054][biodb::testThat]
biodb.INFO [2025-03-26 18:17:36.054][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-26 18:17:36.054][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:36.054][biodb::testThat]
biodb.DEBUG[2025-03-26 18:17:36.055][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-26 18:17:36.057][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:36.057][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-26 18:17:36.058][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:36.058][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-26 18:17:36.059][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:36.061][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:36.061][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:36.061][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-26 18:17:36.390][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-26 18:17:36.719][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:36.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-26 18:17:36.721][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-26 18:17:36.725][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 18:17:36.725][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-26 18:17:36.725][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-26 18:17:36.726][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 18:17:36.726][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.726][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.727][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-26 18:17:36.729][biodb::testContext]
biodb.INFO [2025-03-26 18:17:36.729][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 18:17:36.729][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-26 18:17:36.729][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 18:17:36.730][biodb::testContext]
biodb.INFO [2025-03-26 18:17:36.731][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 18:17:36.731][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 18:17:36.733][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:17:36.733][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 18:17:36.733][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 18:17:36.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.734][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 18:17:36.735][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 18:17:36.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.736][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 18:17:36.736][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 18:17:36.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.737][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[2025-03-26 18:17:36.737][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 18:17:36.737][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 18:17:36.737][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 18:17:36.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.738][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 18:17:36.739][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 18:17:36.739][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 18:17:36.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.740][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 18:17:36.740][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 18:17:36.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.741][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 18:17:36.741][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 18:17:36.742][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 18:17:36.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.743][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 18:17:36.743][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 18:17:36.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.744][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 18:17:36.744][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 18:17:36.744][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 18:17:36.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.745][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 18:17:36.745][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 18:17:36.746][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 18:17:36.746][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 18:17:36.746][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 18:17:36.747][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 18:17:36.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.747][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 18:17:36.748][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 18:17:36.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.749][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 18:17:36.749][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 18:17:36.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.750][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 18:17:36.750][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 18:17:36.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.751][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 18:17:36.751][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 18:17:36.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.752][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 18:17:36.753][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 18:17:36.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.754][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 18:17:36.754][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 18:17:36.761][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 18:17:36.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.762][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 18:17:36.762][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 18:17:36.763][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 18:17:36.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.764][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 18:17:36.764][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.764][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-26 18:17:36.765][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.765][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:36.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.766][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.766][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.766][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 18:17:36.767][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:36.767][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.767][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 18:17:36.767][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:36.768][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.768][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.768][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:17:36.768][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:17:36.768][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:17:36.768][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 18:17:36.768][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 18:17:36.769][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:36.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.769][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:36.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.774][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.775][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.775][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.775][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:36.775][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:36.776][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.776][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.776][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 18:17:36.777][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.777][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 18:17:36.777][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.778][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:36.778][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.778][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.778][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.779][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.779][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 18:17:36.779][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:36.779][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.780][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 18:17:36.780][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:36.780][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.780][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.781][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:17:36.781][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:17:36.781][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:17:36.781][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 18:17:36.781][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 18:17:36.781][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:36.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.781][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.782][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:36.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.782][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.782][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.783][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.783][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:36.783][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:36.783][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.784][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.784][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 18:17:36.784][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.785][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-26 18:17:36.785][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.785][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:36.785][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.786][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.786][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.786][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.786][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 18:17:36.787][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:36.787][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.787][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 18:17:36.787][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:36.788][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.788][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.788][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.788][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:36.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.789][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:36.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.790][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.790][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.790][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:36.791][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:36.791][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.791][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.791][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 18:17:36.792][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.792][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 18:17:36.792][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.793][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:36.793][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.793][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.793][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.794][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.794][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 18:17:36.794][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:36.794][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.795][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 18:17:36.795][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:36.795][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.795][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.795][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.796][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 18:17:36.796][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.796][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:36.797][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.797][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.797][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.797][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.798][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:36.798][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:36.798][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.798][self$setPropertyValue]
biodb.DEBUG[2025-03-26 18:17:36.799][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:17:36.799][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.816][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[2025-03-26 18:17:36.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.818][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 18:17:36.818][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 18:17:36.819][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 18:17:36.819][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 18:17:36.820][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 18:17:36.820][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 18:17:36.820][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 18:17:36.821][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 18:17:36.821][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 18:17:36.821][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 18:17:36.822][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 18:17:36.822][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 18:17:36.822][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 18:17:36.823][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 18:17:36.823][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 18:17:36.824][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 18:17:36.824][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 18:17:36.824][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 18:17:36.825][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 18:17:36.825][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 18:17:36.825][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 18:17:36.826][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 18:17:36.826][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 18:17:36.827][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 18:17:36.827][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 18:17:36.827][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 18:17:36.828][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 18:17:36.828][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 18:17:36.828][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 18:17:36.829][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 18:17:36.829][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 18:17:36.829][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 18:17:36.830][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 18:17:36.830][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 18:17:36.831][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 18:17:36.831][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 18:17:36.831][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 18:17:36.832][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 18:17:36.832][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 18:17:36.832][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 18:17:36.833][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 18:17:36.833][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 18:17:36.833][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 18:17:36.834][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 18:17:36.834][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 18:17:36.834][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 18:17:36.835][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 18:17:36.835][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 18:17:36.836][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 18:17:36.836][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 18:17:36.836][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 18:17:36.837][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 18:17:36.837][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 18:17:36.837][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 18:17:36.838][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 18:17:36.838][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 18:17:36.838][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 18:17:36.839][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 18:17:36.839][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 18:17:36.840][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 18:17:36.840][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 18:17:36.840][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 18:17:36.841][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 18:17:36.841][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 18:17:36.841][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 18:17:36.842][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 18:17:36.842][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 18:17:36.842][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 18:17:36.843][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 18:17:36.843][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 18:17:36.844][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 18:17:36.844][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 18:17:36.844][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 18:17:36.845][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 18:17:36.845][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 18:17:36.845][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 18:17:36.846][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 18:17:36.846][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 18:17:36.846][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 18:17:36.847][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 18:17:36.847][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 18:17:36.848][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 18:17:36.848][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 18:17:36.848][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 18:17:36.849][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 18:17:36.849][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 18:17:36.850][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.850][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.861][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[2025-03-26 18:17:36.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.868][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[2025-03-26 18:17:36.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.876][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.DEBUG[2025-03-26 18:17:36.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 18:17:36.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.881][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-26 18:17:36.882][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-26 18:17:36.882][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.883][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.883][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.883][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 18:17:36.884][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.884][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.884][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.884][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-26 18:17:36.885][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 18:17:36.885][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 18:17:36.885][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.885][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-26 18:17:36.886][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 18:17:36.887][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 18:17:36.887][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 18:17:36.887][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 18:17:36.887][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 18:17:36.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.887][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.888][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 18:17:36.888][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 18:17:36.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 18:17:36.888][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 18:17:36.889][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:36.889][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-26 18:17:36.889][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 18:17:36.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 18:17:36.890][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 18:17:36.890][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-26 18:17:36.890][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-26 18:17:36.890][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 18:17:36.891][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 18:17:36.891][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-26 18:17:36.892][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 18:17:36.892][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 18:17:36.892][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 18:17:36.894][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-26 18:17:36.894][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-26 18:17:36.894][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-26 18:17:36.895][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-26 18:17:36.895][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 18:17:36.895][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 18:17:36.896][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-26 18:17:36.896][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-26 18:17:36.896][biodb::testThat]
biodb.INFO [2025-03-26 18:17:36.897][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-26 18:17:36.897][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 18:17:36.897][biodb::testThat]
biodb.DEBUG[2025-03-26 18:17:36.898][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-26 18:17:36.899][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:36.900][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-26 18:17:36.900][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:36.901][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-26 18:17:36.902][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 18:17:36.903][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 18:17:36.903][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-26 18:17:36.904][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 18:17:36.904][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-26 18:17:36.906][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-26 18:17:36.906][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 18:17:36.907][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-26 18:17:36.907][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 18:17:36.908][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 18:17:36.908][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 18:17:36.908][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 18:17:36.908][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 18:17:36.909][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 18:17:36.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:36.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:36.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:36.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:36.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:36.912][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:36.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 18:17:36.913][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-26 18:17:36.914][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 18:17:36.914][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 18:17:36.915][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-26 18:17:38.725][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-26 18:17:39.869][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 18:17:39.870][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-26 18:17:39.871][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-26 18:17:39.872][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-26 18:17:39.872][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 18:17:39.873][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 18:17:39.873][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 18:17:39.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 18:17:39.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:39.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:39.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:39.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:39.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:39.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 18:17:39.878][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:39.879][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:39.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:39.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:39.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.881][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:39.881][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:39.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.882][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.882][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 18:17:39.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 18:17:39.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.883][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:39.883][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:39.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.884][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.884][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 18:17:39.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 18:17:39.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.885][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 18:17:39.886][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 18:17:39.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.887][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 18:17:39.887][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 18:17:39.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.887][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.888][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:39.888][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:39.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.888][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.889][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:39.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 18:17:39.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.890][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:39.890][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:39.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.891][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.891][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 18:17:39.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 18:17:39.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.892][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:39.892][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:39.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.893][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:39.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 18:17:39.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.894][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:39.894][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:39.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 18:17:39.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 18:17:39.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.897][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:39.897][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:39.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.897][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.898][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 18:17:39.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 18:17:39.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.899][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:39.899][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:39.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.900][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.900][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 18:17:39.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 18:17:39.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:39.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:39.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:39.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:39.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:39.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:39.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 18:17:39.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 18:17:39.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:39.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:39.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:39.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:39.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:39.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:39.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:39.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:39.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:39.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:39.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 18:17:39.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 18:17:39.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 18:17:39.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 18:17:39.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 18:17:39.911][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-26 18:17:39.913][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 18:17:39.913][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-26 18:17:39.914][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-26 18:17:39.919][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 18:17:39.919][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 18:17:39.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 18:17:39.919][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 18:17:39.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 18:17:39.920][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 18:17:39.920][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
  5.602   0.404  49.886

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	0.766	0.263	2.464
ChebiEntry	0.110	0.007	0.120