Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-09 17:42 -0400 (Tue, 09 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4709
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 200/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-07 14:00 -0400 (Sun, 07 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_19
git_last_commit: fad38a4
git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbChebi on kjohnson1

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

raw results


Summary

Package: biodbChebi
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.10.0.tar.gz
StartedAt: 2024-07-08 12:45:44 -0400 (Mon, 08 Jul 2024)
EndedAt: 2024-07-08 12:47:04 -0400 (Mon, 08 Jul 2024)
EllapsedTime: 80.0 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-07-08 12:46:31.189][biodb::testContext]
biodb.INFO [2024-07-08 12:46:31.194][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 12:46:31.195][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-07-08 12:46:31.196][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 12:46:31.197][biodb::testContext]
biodb.INFO [2024-07-08 12:46:31.206][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-08 12:46:31.209][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-08 12:46:31.219][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:31.221][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-08 12:46:31.222][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-08 12:46:31.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.225][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-08 12:46:31.246][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-08 12:46:31.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.250][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-08 12:46:31.251][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-08 12:46:31.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.254][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-08 12:46:31.255][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-08 12:46:31.256][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-08 12:46:31.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.276][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-08 12:46:31.277][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-08 12:46:31.278][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-08 12:46:31.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.281][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-08 12:46:31.282][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-08 12:46:31.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.285][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-08 12:46:31.286][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-08 12:46:31.287][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-08 12:46:31.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.290][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-08 12:46:31.290][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-08 12:46:31.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.293][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-08 12:46:31.294][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-08 12:46:31.295][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-08 12:46:31.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.298][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-08 12:46:31.299][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-08 12:46:31.300][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-08 12:46:31.300][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-08 12:46:31.301][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-08 12:46:31.302][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-08 12:46:31.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.305][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-08 12:46:31.306][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-08 12:46:31.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.309][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-08 12:46:31.310][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-08 12:46:31.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.313][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-08 12:46:31.313][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-08 12:46:31.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.316][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-08 12:46:31.317][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-08 12:46:31.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.320][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-08 12:46:31.321][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-08 12:46:31.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.324][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-08 12:46:31.325][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-08 12:46:31.342][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-08 12:46:31.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.345][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-08 12:46:31.346][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-08 12:46:31.347][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-08 12:46:31.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.354][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-08 12:46:31.390][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.407][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-08 12:46:31.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.409][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:31.410][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.411][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.412][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.412][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.413][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 12:46:31.414][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:31.415][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.416][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-08 12:46:31.417][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:31.418][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.418][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.420][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:31.420][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:31.420][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:31.420][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 12:46:31.420][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 12:46:31.421][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:31.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:31.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:31.424][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:31.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:31.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:31.428][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.429][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.431][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:31.432][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:31.433][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.434][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.435][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-08 12:46:31.437][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.438][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 12:46:31.439][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.439][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:31.440][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.441][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.442][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.443][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.444][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 12:46:31.444][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:31.445][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.446][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-08 12:46:31.447][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:31.448][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.448][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.449][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:31.449][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:31.449][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:31.449][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 12:46:31.449][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 12:46:31.450][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:31.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:31.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:31.452][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:31.453][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:31.454][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:31.455][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.455][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.456][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:31.457][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:31.458][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.459][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.459][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-08 12:46:31.461][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.462][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-08 12:46:31.463][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.464][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:31.465][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.466][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.467][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.467][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.468][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 12:46:31.477][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:31.477][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.478][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-08 12:46:31.479][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:31.480][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.481][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.482][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.482][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:31.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:31.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:31.485][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:31.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:31.486][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:31.487][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.488][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.488][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:31.489][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:31.490][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.491][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.492][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-08 12:46:31.493][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.494][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 12:46:31.495][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.496][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:31.497][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.497][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.498][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.499][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.500][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 12:46:31.500][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:31.501][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.502][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-08 12:46:31.503][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:31.504][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.504][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.505][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.506][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:31.507][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:31.508][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:31.508][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:31.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:31.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:31.511][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.511][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.512][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:31.513][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:31.514][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.514][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:31.520][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:31.520][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.570][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.DEBUG[2024-07-08 12:46:31.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.581][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-08 12:46:31.588][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-08 12:46:31.589][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-08 12:46:31.590][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-08 12:46:31.592][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 12:46:31.593][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-08 12:46:31.594][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-08 12:46:31.595][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-08 12:46:31.596][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-08 12:46:31.597][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-08 12:46:31.598][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 12:46:31.599][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-08 12:46:31.601][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-08 12:46:31.602][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-08 12:46:31.603][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-08 12:46:31.604][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-08 12:46:31.605][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-08 12:46:31.606][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-08 12:46:31.607][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 12:46:31.609][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-08 12:46:31.610][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-08 12:46:31.611][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-08 12:46:31.612][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-08 12:46:31.613][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-08 12:46:31.614][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-08 12:46:31.616][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-08 12:46:31.617][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-08 12:46:31.618][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-08 12:46:31.619][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-08 12:46:31.620][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-08 12:46:31.621][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-08 12:46:31.622][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-08 12:46:31.624][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-08 12:46:31.625][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-08 12:46:31.626][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-08 12:46:31.627][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-08 12:46:31.628][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-08 12:46:31.630][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-08 12:46:31.631][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-08 12:46:31.632][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-08 12:46:31.634][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-08 12:46:31.635][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-08 12:46:31.636][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-08 12:46:31.638][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-08 12:46:31.645][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-08 12:46:31.647][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-08 12:46:31.648][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-08 12:46:31.649][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-08 12:46:31.650][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-08 12:46:31.651][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-08 12:46:31.653][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-08 12:46:31.654][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-08 12:46:31.655][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-08 12:46:31.656][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-08 12:46:31.657][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-08 12:46:31.658][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-08 12:46:31.660][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-08 12:46:31.661][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-08 12:46:31.662][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-08 12:46:31.663][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-08 12:46:31.664][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-08 12:46:31.665][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-08 12:46:31.666][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-08 12:46:31.668][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-08 12:46:31.669][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-08 12:46:31.670][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-08 12:46:31.671][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 12:46:31.672][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 12:46:31.673][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-08 12:46:31.675][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-08 12:46:31.676][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-08 12:46:31.677][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-08 12:46:31.678][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-08 12:46:31.680][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-08 12:46:31.681][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-08 12:46:31.682][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-08 12:46:31.683][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-08 12:46:31.684][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-08 12:46:31.685][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-08 12:46:31.687][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-08 12:46:31.688][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-08 12:46:31.689][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-08 12:46:31.690][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-08 12:46:31.696][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-08 12:46:31.698][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-08 12:46:31.703][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:31.704][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.705][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.752][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[2024-07-08 12:46:31.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:31.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:31.797][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-08 12:46:31.814][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-08 12:46:31.817][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.818][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.819][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.820][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:31.820][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.821][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.822][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.823][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-08 12:46:31.824][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-08 12:46:31.825][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:31.826][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.826][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-08 12:46:31.828][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-08 12:46:31.829][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-08 12:46:31.830][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:31.831][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:31.831][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:31.831][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:31.832][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-08 12:46:31.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:31.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:31.835][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:31.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:31.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:31.837][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:31.838][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:31.838][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-08 12:46:31.839][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:31.840][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:31.841][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:31.841][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-08 12:46:31.841][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-08 12:46:31.848][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 12:46:31.850][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 12:46:31.851][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-08 12:46:31.853][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 12:46:31.854][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 12:46:31.856][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 12:46:31.889][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-08 12:46:31.891][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-08 12:46:31.896][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-08 12:46:31.902][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-08 12:46:31.907][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-08 12:46:31.908][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-08 12:46:31.910][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-08 12:46:31.910][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-08 12:46:31.924][biodb::testThat]
biodb.INFO [2024-07-08 12:46:31.925][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-08 12:46:31.927][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:31.927][biodb::testThat]
biodb.TRACE[2024-07-08 12:46:31.933][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-07-08 12:46:31.935][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:31.940][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:31.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:31.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:31.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:31.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:31.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:31.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:31.971][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.TRACE[2024-07-08 12:46:31.984][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:31.986][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:31.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:31.988][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:31.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.006][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:32.007][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:32.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.009][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.038][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:32.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:32.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.042][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:32.043][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:32.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.045][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.046][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:32.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:32.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.061][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.063][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.065][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.069][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.070][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.072][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.077][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.078][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.080][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.081][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.084][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:32.085][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.087][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.088][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:32.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.092][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.094][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.098][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:32.099][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:32.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.101][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:32.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:32.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.106][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:32.107][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.108][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.109][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:32.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.113][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:32.114][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:32.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.115][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.116][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:32.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:32.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.120][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:32.188][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-07-08 12:46:32.192][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.276][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.287][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 12:46:32.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 12:46:32.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.290][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 12:46:32.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 12:46:32.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.293][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-08 12:46:32.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-08 12:46:32.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.297][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-08 12:46:32.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-08 12:46:32.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.409][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.410][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.412][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.444][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.445][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.446][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:32.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:32.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:32.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:32.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:32.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:32.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:32.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.471][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:32.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:32.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.473][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:32.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:32.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:32.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:32.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.489][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:32.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:32.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.493][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:32.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:32.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.496][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:32.497][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:32.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.499][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:32.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:32.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.521][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.522][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.523][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.550][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.551][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.553][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.566][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:32.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:32.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.570][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:32.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:32.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.573][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:32.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:32.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.576][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:32.584][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:32.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.587][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.588][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:32.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:32.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.600][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.604][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.608][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.611][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.612][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.613][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.614][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.627][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.632][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.635][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.639][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.640][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.641][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.642][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.654][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:32.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:32.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.658][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:32.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:32.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.661][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:32.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:32.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.665][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:32.666][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:32.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.667][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.668][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:32.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:32.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.680][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.684][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.690][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.691][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.692][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.693][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.712][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.716][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.717][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.719][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.731][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.732][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.734][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.745][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:32.747][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:32.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.749][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.754][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:32.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:32.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.757][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.762][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.764][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.765][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.770][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.771][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.773][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.778][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.779][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.781][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.786][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.787][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.788][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.794][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.795][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.796][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.801][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.803][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:32.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.805][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.810][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:32.811][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:32.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.813][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.818][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:32.819][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:32.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.821][ef$get] fields variable is a list.
biodb.INFO [2024-07-08 12:46:32.830][biodb::testThat]
biodb.INFO [2024-07-08 12:46:32.831][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-08 12:46:32.832][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:32.833][biodb::testThat]
biodb.DEBUG[2024-07-08 12:46:32.847][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-07-08 12:46:32.857][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:32.862][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-07-08 12:46:32.864][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:32.865][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-07-08 12:46:32.866][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:32.890][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:32.891][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:32.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:32.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:32.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:32.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:32.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:32.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:32.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:32.906][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.907][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.908][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:32.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:32.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.937][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:32.939][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:32.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.940][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.942][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:32.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:32.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.946][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:32.947][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:32.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.948][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.949][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:32.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:32.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.953][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.954][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.955][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:32.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:32.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.960][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.961][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.963][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:32.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.970][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.971][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.973][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.975][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:32.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.979][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:32.980][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.982][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.984][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:32.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:32.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.989][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.990][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.992][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:32.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:32.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:32.999][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:33.000][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:33.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.002][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:33.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:33.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.008][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:33.009][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:33.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.010][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.011][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:33.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:33.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.015][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:33.015][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:33.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.017][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.018][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:33.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:33.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:33.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:33.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:33.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:33.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:33.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:33.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:33.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:33.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:33.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:33.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:33.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:33.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:33.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:33.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:33.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:33.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:33.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:33.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:33.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:33.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:33.052][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-07-08 12:46:33.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-08 12:46:33.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-08 12:46:33.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-08 12:46:33.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-08 12:46:33.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-08 12:46:33.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-08 12:46:33.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 12:46:33.077][biodb::testThat]
biodb.INFO [2024-07-08 12:46:33.078][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-08 12:46:33.079][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:33.080][biodb::testThat]
biodb.TRACE[2024-07-08 12:46:33.084][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:33.085][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:33.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.086][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:33.088][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-07-08 12:46:33.115][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:33.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:33.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.119][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:33.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:33.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:33.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:33.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:33.130][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-07-08 12:46:33.136][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-08 12:46:33.157][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:33.173][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-08 12:46:33.175][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:33.177][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-08 12:46:33.201][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:33.205][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:33.206][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:33.208][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:33.571][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:33.805][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:33.807][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-07-08 12:46:33.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-07-08 12:46:33.827][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-07-08 12:46:33.840][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:33.842][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:33.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.843][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.844][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:33.845][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:33.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.862][ef$get] fields variable is a list.
biodb.INFO [2024-07-08 12:46:33.868][biodb::testThat]
biodb.INFO [2024-07-08 12:46:33.869][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-08 12:46:33.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:33.871][biodb::testThat]
biodb.TRACE[2024-07-08 12:46:33.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:33.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:33.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:33.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:33.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:33.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:33.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:33.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:33.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:33.965][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:33.970][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:33.971][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-08 12:46:33.972][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:33.974][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-07-08 12:46:34.000][biodb::testThat]
biodb.INFO [2024-07-08 12:46:34.001][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-08 12:46:34.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:34.003][biodb::testThat]
biodb.TRACE[2024-07-08 12:46:34.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:34.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:34.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:34.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:34.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:34.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:34.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:34.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:34.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:34.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:34.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:34.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:34.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.047][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 12:46:34.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 12:46:34.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.050][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 12:46:34.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 12:46:34.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.054][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-08 12:46:34.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-08 12:46:34.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.057][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-08 12:46:34.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-08 12:46:34.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:34.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:34.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:34.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:34.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.087][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:34.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:34.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.090][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:34.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:34.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:34.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:34.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:34.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:34.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.100][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 12:46:34.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 12:46:34.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.110][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-08 12:46:34.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-08 12:46:34.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.114][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-08 12:46:34.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-08 12:46:34.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.117][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-08 12:46:34.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-08 12:46:34.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 12:46:34.129][biodb::testThat]
biodb.INFO [2024-07-08 12:46:34.130][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-08 12:46:34.131][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:34.133][biodb::testThat]
biodb.INFO [2024-07-08 12:46:34.143][biodb::testThat]
biodb.INFO [2024-07-08 12:46:34.144][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-08 12:46:34.145][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:34.146][biodb::testThat]
biodb.INFO [2024-07-08 12:46:34.155][biodb::testThat]
biodb.INFO [2024-07-08 12:46:34.156][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-08 12:46:34.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:34.157][biodb::testThat]
biodb.DEBUG[2024-07-08 12:46:34.161][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-07-08 12:46:34.380][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-07-08 12:46:34.677][biodb::testThat]
biodb.INFO [2024-07-08 12:46:34.678][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-08 12:46:34.679][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:34.680][biodb::testThat]
biodb.DEBUG[2024-07-08 12:46:34.798][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-07-08 12:46:34.900][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:34.901][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:34.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.903][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.904][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:34.904][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:34.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.906][ef$get] fields variable is a list.
biodb.INFO [2024-07-08 12:46:34.908][biodb::testThat]
biodb.INFO [2024-07-08 12:46:34.909][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-07-08 12:46:34.910][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:34.911][biodb::testThat]
biodb.TRACE[2024-07-08 12:46:34.923][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:34.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:34.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.926][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:34.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:34.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:34.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:34.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:34.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:34.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:35.035][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:35.039][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:35.041][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-08 12:46:35.043][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:35.045][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-08 12:46:35.141][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:35.145][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:35.146][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-08 12:46:35.147][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:35.148][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-07-08 12:46:35.164][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-08 12:46:35.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-08 12:46:35.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:35.199][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:35.224][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:35.225][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:35.241][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:35.323][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:35.400][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:35.403][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-07-08 12:46:35.407][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-07-08 12:46:35.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:35.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:35.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:35.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:35.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:35.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:35.420][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[2024-07-08 12:46:35.421][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-07-08 12:46:35.468][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:35.476][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-07-08 12:46:35.481][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:35.482][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:35.483][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:35.484][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:35.485][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:35.486][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:35.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:35.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:35.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:35.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:35.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:35.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:35.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:35.501][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-07-08 12:46:35.504][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:35.505][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:35.507][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-07-08 12:46:35.588][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-07-08 12:46:35.659][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:35.661][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-07-08 12:46:35.666][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-07-08 12:46:35.668][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-07-08 12:46:35.670][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:35.671][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:35.672][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:35.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:35.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:35.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:35.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:35.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:35.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:35.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:35.687][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:35.688][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:35.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.690][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:35.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:35.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.694][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:35.695][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:35.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.697][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.698][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:35.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:35.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.701][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:35.702][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:35.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.704][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:35.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:35.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.709][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:35.710][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:35.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.711][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:35.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:35.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.716][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:35.717][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:35.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.718][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:35.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:35.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.723][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:35.724][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:35.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.725][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.726][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:35.727][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.729][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.730][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:35.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.734][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:35.735][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:35.735][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.736][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:35.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:35.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.751][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:35.752][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:35.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.754][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:35.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:35.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.759][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:35.760][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:35.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.762][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.763][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:35.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:35.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.767][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:35.768][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:35.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.770][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.772][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:35.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:35.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:35.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:35.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:35.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:35.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:35.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:35.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:35.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:35.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:35.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:35.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:35.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:35.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:35.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:35.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:35.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:35.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:35.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:35.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:35.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:35.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:35.809][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-07-08 12:46:35.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:35.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:35.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:35.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:35.829][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:35.833][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:35.834][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:35.836][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:35.909][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:35.983][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:35.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-07-08 12:46:35.990][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-07-08 12:46:36.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:36.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:36.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:36.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:36.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:36.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:36.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:36.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:36.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:36.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:36.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:36.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:36.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:36.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:36.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:36.048][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-07-08 12:46:36.049][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:36.050][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-07-08 12:46:36.052][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:36.053][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:36.054][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:36.055][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:36.055][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:36.056][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:36.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:36.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:36.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:36.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:36.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:36.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:36.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:36.081][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-07-08 12:46:36.084][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:36.085][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-08 12:46:36.086][rule$waitAsNeeded] Wait 0.154227 second(s).
biodb.TRACE[2024-07-08 12:46:36.392][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-07-08 12:46:36.475][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-07-08 12:46:36.561][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:36.564][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-07-08 12:46:36.568][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-07-08 12:46:36.571][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-07-08 12:46:36.572][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:36.573][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:36.575][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:36.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:36.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:36.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:36.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:36.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:36.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:36.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:36.600][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:36.601][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:36.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.602][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:36.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:36.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.607][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:36.608][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:36.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.610][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.611][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:36.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:36.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.614][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:36.615][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:36.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.617][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.618][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:36.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:36.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.622][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:36.623][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:36.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.624][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.625][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:36.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:36.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.629][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:36.629][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:36.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.632][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:36.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:36.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.637][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:36.638][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:36.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.640][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.641][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:36.642][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.645][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.646][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:36.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.649][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:36.651][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:36.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.655][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:36.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:36.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.661][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:36.662][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:36.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.664][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:36.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:36.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.669][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:36.670][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:36.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.672][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.673][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:36.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:36.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.677][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:36.678][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:36.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.679][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.680][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:36.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:36.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:36.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:36.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:36.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:36.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:36.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:36.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:36.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:36.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:36.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:36.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:36.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:36.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:36.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:36.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:36.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:36.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:36.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:36.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:36.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:36.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:36.724][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-07-08 12:46:36.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:36.755][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:36.759][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:36.760][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-08 12:46:36.761][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:36.763][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-08 12:46:36.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:36.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:36.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:36.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:36.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:36.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:36.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:36.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:36.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:36.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:36.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:36.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:36.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:36.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:36.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:36.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:36.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:36.799][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[2024-07-08 12:46:36.800][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-07-08 12:46:36.801][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:36.802][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-07-08 12:46:36.803][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:36.804][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:36.805][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:36.806][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:36.807][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:36.808][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:36.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:36.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:36.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:36.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:36.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:36.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:36.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:36.828][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-07-08 12:46:36.831][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:36.832][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:36.834][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-07-08 12:46:36.913][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-07-08 12:46:36.986][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:36.989][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-07-08 12:46:36.993][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-07-08 12:46:36.996][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-07-08 12:46:36.998][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:36.999][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:37.000][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:37.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:37.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:37.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:37.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:37.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:37.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:37.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:37.017][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.018][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.020][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.024][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:37.025][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:37.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.027][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.028][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:37.029][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:37.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.030][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.031][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:37.032][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:37.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.034][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.035][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:37.036][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:37.037][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.037][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.038][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:37.039][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:37.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.041][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.042][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:37.043][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.044][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.045][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:37.046][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:37.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.048][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.049][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:37.050][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:37.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.051][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:37.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:37.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.056][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:37.056][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:37.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.058][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.059][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:37.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:37.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.062][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:37.063][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:37.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.065][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:37.109][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-07-08 12:46:37.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:37.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:37.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:37.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:37.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:37.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:37.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:37.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:37.139][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-07-08 12:46:37.140][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:37.141][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-07-08 12:46:37.143][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:37.144][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:37.145][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:37.145][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:37.146][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:37.147][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:37.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:37.151][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:37.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:37.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:37.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:37.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:37.160][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[2024-07-08 12:46:37.161][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-07-08 12:46:37.164][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:37.165][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:37.166][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-07-08 12:46:37.248][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-07-08 12:46:37.330][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:37.333][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-07-08 12:46:37.337][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-07-08 12:46:37.340][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-07-08 12:46:37.343][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:37.344][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:37.346][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:37.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:37.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:37.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:37.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:37.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:37.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:37.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:37.373][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.375][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.377][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.382][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:37.383][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:37.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.385][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.386][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:37.387][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:37.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.389][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.390][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:37.391][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:37.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.393][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.394][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:37.395][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:37.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.396][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.397][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:37.398][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:37.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.400][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.401][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:37.402][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.404][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.405][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:37.406][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:37.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.407][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.409][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:37.409][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:37.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.411][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:37.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:37.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.416][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:37.417][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:37.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.419][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.420][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:37.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:37.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.424][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:37.424][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:37.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.426][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:37.464][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-07-08 12:46:37.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:37.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:37.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:37.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:37.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:37.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:37.541][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:37.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:37.543][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-07-08 12:46:37.544][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:37.545][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-07-08 12:46:37.547][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:37.548][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:37.549][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:37.549][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:37.550][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:37.551][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:37.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:37.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:37.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:37.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:37.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:37.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:37.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:37.566][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-07-08 12:46:37.569][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:37.570][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:37.571][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-07-08 12:46:37.644][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-07-08 12:46:37.718][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:37.721][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-07-08 12:46:37.725][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-07-08 12:46:37.729][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-07-08 12:46:37.731][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:37.732][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:37.733][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:37.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:37.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:37.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:37.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:37.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:37.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:37.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:37.748][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.749][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.750][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.755][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:37.756][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:37.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.758][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.759][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:37.760][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:37.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.762][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.763][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:37.764][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:37.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.766][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.767][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:37.768][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:37.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.769][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.771][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:37.771][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:37.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.773][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.774][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:37.775][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.783][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.789][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:37.790][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:37.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.792][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.794][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:37.795][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:37.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.797][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:37.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:37.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.802][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:37.804][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:37.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.805][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.807][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:37.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:37.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.811][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:37.812][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:37.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.814][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:37.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:37.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:37.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:37.852][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-07-08 12:46:37.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:37.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:37.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:37.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:37.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:37.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:37.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:37.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:37.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:37.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:37.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:37.880][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-07-08 12:46:37.881][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:37.883][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-07-08 12:46:37.884][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:37.885][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:37.886][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:37.887][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:37.888][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:37.889][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:37.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:37.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:37.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:37.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:37.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:37.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:37.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:37.910][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-07-08 12:46:37.913][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:37.914][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:37.916][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-07-08 12:46:38.000][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-07-08 12:46:38.071][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:38.074][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-07-08 12:46:38.078][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-07-08 12:46:38.080][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-07-08 12:46:38.082][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:38.084][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:38.085][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:38.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:38.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:38.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:38.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:38.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:38.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:38.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:38.099][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.100][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.102][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.106][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:38.107][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:38.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.109][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.110][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:38.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:38.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.113][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:38.114][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:38.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.116][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.117][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:38.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:38.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.120][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:38.121][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:38.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.123][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.124][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:38.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:38.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.127][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.128][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.130][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.134][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:38.135][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:38.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.136][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.138][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:38.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:38.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.141][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:38.142][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.143][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.144][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:38.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.148][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.149][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.150][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.155][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:38.155][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:38.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.157][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.169][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:38.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:38.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.173][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:38.174][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:38.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.176][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.177][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:38.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:38.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.181][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:38.181][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:38.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.183][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.184][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:38.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:38.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:38.221][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-07-08 12:46:38.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:38.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:38.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:38.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:38.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:38.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:38.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:38.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:38.242][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-07-08 12:46:38.243][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:38.244][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-07-08 12:46:38.246][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:38.247][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:38.247][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:38.248][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:38.249][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:38.250][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:38.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:38.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:38.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:38.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:38.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:38.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:38.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:38.264][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-07-08 12:46:38.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:38.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:38.276][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-07-08 12:46:38.366][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-07-08 12:46:38.445][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:38.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-07-08 12:46:38.452][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-07-08 12:46:38.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-07-08 12:46:38.457][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:38.458][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:38.459][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:38.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:38.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:38.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:38.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:38.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:38.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:38.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:38.475][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.476][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.477][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.478][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.483][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:38.484][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:38.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.486][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.487][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:38.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:38.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.491][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:38.493][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:38.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.495][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:38.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:38.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.500][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:38.501][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:38.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.503][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:38.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:38.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.508][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.509][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.510][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.516][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:38.517][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:38.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.518][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.519][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:38.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:38.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.523][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:38.524][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.526][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.528][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:38.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.532][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.533][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.534][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.539][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:38.540][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:38.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.541][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:38.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:38.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.546][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:38.547][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:38.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.548][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.549][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:38.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:38.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.553][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:38.564][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:38.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.567][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:38.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:38.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.589][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:38.605][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-07-08 12:46:38.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:38.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:38.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:38.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:38.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:38.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:38.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:38.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:38.626][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-07-08 12:46:38.627][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:38.629][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-07-08 12:46:38.630][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:38.631][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:38.632][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:38.633][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:38.633][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:38.634][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:38.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:38.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:38.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:38.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:38.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:38.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:38.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:38.648][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-07-08 12:46:38.651][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:38.652][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:38.654][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-07-08 12:46:38.733][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-07-08 12:46:38.806][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:38.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-07-08 12:46:38.813][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-07-08 12:46:38.816][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-07-08 12:46:38.817][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:38.829][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:38.831][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:38.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:38.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:38.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:38.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:38.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:38.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:38.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:38.846][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.847][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.848][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.853][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:38.854][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:38.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.856][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:38.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:38.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.860][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:38.861][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:38.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.863][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.864][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:38.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:38.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.867][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:38.868][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:38.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.870][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:38.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:38.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.875][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.876][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.877][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:38.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.882][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:38.883][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:38.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.884][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.885][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:38.886][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.888][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.889][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:38.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.892][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.893][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.895][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:38.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.899][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:38.900][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:38.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.902][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:38.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:38.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.906][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:38.907][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:38.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.909][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.910][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:38.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:38.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.913][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:38.914][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:38.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.916][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.917][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:38.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:38.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:38.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:38.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:38.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:38.967][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-07-08 12:46:38.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:38.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:38.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:38.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:38.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:38.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:38.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:38.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:38.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:38.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:38.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:38.991][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-07-08 12:46:38.992][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:38.993][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-07-08 12:46:38.994][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:38.995][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:38.996][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:38.997][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:38.998][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:39.000][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:39.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:39.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:39.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:39.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:39.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:39.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:39.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:39.015][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-07-08 12:46:39.018][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:39.019][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:39.020][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-07-08 12:46:39.101][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-07-08 12:46:39.177][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:39.179][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-07-08 12:46:39.183][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-07-08 12:46:39.185][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-07-08 12:46:39.187][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:39.188][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:39.189][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:39.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:39.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:39.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:39.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:39.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:39.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:39.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:39.203][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.204][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.214][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.220][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:39.221][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:39.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.223][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.224][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:39.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:39.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.227][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:39.228][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:39.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.230][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.231][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:39.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:39.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.234][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:39.235][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:39.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.237][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.238][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:39.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:39.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.241][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.242][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.243][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.248][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:39.249][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:39.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.250][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.251][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:39.252][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.253][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.255][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:39.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.258][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.259][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.260][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.264][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:39.265][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:39.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.267][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.268][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:39.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:39.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.272][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:39.272][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:39.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.274][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.275][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:39.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:39.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.278][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:39.279][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:39.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.280][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.282][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:39.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:39.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:39.324][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-07-08 12:46:39.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:39.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:39.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:39.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:39.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:39.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:39.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:39.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:39.347][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-07-08 12:46:39.348][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:39.349][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-07-08 12:46:39.350][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:39.351][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:39.352][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:39.353][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:39.354][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:39.355][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:39.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:39.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:39.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:39.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:39.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:39.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:39.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:39.370][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-07-08 12:46:39.373][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:39.374][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:39.375][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-07-08 12:46:39.446][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-07-08 12:46:39.518][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:39.521][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-07-08 12:46:39.525][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-07-08 12:46:39.528][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-07-08 12:46:39.529][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:39.530][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:39.531][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:39.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:39.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:39.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:39.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:39.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:39.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:39.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:39.545][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.546][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.548][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.552][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:39.553][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:39.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.555][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.556][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:39.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:39.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.559][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:39.560][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:39.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.572][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.573][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:39.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:39.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.577][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:39.578][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:39.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.580][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:39.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:39.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.584][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.585][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.587][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.592][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:39.593][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:39.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.594][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.596][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:39.597][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.598][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.600][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:39.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.604][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.607][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.613][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:39.613][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:39.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.615][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:39.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:39.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.620][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:39.621][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:39.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.622][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.624][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:39.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:39.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.627][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:39.628][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:39.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.630][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.631][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:39.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:39.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:39.671][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-07-08 12:46:39.679][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:39.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:39.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:39.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:39.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:39.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:39.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:39.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:39.703][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-07-08 12:46:39.704][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:39.705][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-07-08 12:46:39.707][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:39.708][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:39.709][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:39.710][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:39.710][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:39.711][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:39.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:39.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:39.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:39.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:39.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:39.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:39.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:39.725][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-07-08 12:46:39.727][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:39.728][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:39.730][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-07-08 12:46:39.805][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-07-08 12:46:39.877][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:39.880][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-07-08 12:46:39.884][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-07-08 12:46:39.887][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-07-08 12:46:39.889][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:39.890][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:39.891][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:39.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:39.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:39.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:39.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:39.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:39.903][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:39.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:39.906][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.907][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.909][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.913][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:39.914][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:39.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.916][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.917][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:39.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:39.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.920][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:39.921][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:39.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.923][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.924][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:39.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:39.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.927][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:39.928][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:39.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.930][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.931][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:39.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:39.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.934][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.942][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.948][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:39.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.953][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:39.954][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:39.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.955][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.956][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:39.957][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.959][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.960][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:39.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:39.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.964][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.965][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.966][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:39.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.971][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:39.972][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:39.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.973][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:39.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:39.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.978][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:39.979][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:39.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.980][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.981][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:39.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:39.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.985][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:39.985][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:39.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.987][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.988][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:39.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:39.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:39.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:39.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:39.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:39.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:39.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:40.024][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-07-08 12:46:40.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:40.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:40.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:40.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:40.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:40.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:40.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:40.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:40.053][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-07-08 12:46:40.053][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:40.055][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-07-08 12:46:40.056][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:40.057][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:40.058][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:40.059][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:40.060][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:40.061][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:40.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:40.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:40.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:40.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:40.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:40.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:40.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:40.075][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-07-08 12:46:40.078][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:40.079][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:40.081][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-07-08 12:46:40.166][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-07-08 12:46:40.247][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:40.249][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-07-08 12:46:40.253][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-07-08 12:46:40.257][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-07-08 12:46:40.259][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:40.261][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:40.262][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:40.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:40.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:40.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:40.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:40.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:40.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:40.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:40.277][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.278][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.280][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.284][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:40.285][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:40.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.287][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.288][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:40.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:40.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.291][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:40.292][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:40.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.294][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:40.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:40.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.298][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:40.299][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:40.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.301][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:40.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:40.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.305][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:40.306][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:40.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.307][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:40.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:40.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.312][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:40.313][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:40.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.314][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.315][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:40.316][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.318][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.329][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:40.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.333][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.334][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.336][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.340][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:40.341][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:40.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.343][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.344][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:40.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:40.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.347][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:40.348][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:40.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.350][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.351][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:40.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:40.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.355][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:40.356][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:40.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.357][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.358][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:40.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:40.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:40.396][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-07-08 12:46:40.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:40.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:40.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:40.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:40.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:40.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:40.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:40.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:40.422][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-07-08 12:46:40.423][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:40.425][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-07-08 12:46:40.427][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:40.428][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:40.429][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:40.430][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:40.439][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:40.440][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:40.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:40.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:40.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:40.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:40.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:40.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:40.454][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.DEBUG[2024-07-08 12:46:40.455][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-07-08 12:46:40.458][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:40.459][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:40.460][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-07-08 12:46:40.538][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-07-08 12:46:40.614][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:40.616][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-07-08 12:46:40.620][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-07-08 12:46:40.623][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-07-08 12:46:40.625][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:40.627][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:40.628][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:40.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:40.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:40.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:40.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:40.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:40.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:40.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:40.642][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.643][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.645][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.650][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:40.651][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:40.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.652][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.654][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:40.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:40.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.657][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:40.658][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:40.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.659][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.661][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:40.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:40.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.665][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:40.666][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:40.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.667][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.668][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:40.669][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:40.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.671][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.672][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:40.673][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:40.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.674][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.675][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:40.676][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.678][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.679][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:40.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.682][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.683][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.684][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.689][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:40.689][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:40.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.691][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:40.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:40.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.694][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:40.701][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:40.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.705][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.706][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:40.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:40.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.708][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:40.708][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:40.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.709][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:40.726][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-07-08 12:46:40.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:40.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:40.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:40.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:40.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:40.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:40.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:40.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:40.745][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-07-08 12:46:40.746][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:40.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-07-08 12:46:40.749][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:40.749][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:40.750][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:40.751][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:40.752][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:40.753][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:40.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:40.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:40.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:40.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:40.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:40.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:40.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:40.767][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-07-08 12:46:40.770][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:40.771][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:40.772][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-07-08 12:46:40.871][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-07-08 12:46:40.939][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:40.941][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-07-08 12:46:40.953][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-07-08 12:46:40.956][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-07-08 12:46:40.956][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:40.957][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:40.958][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:40.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:40.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:40.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:40.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:40.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:40.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:40.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:40.965][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.966][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.966][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.968][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:40.969][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:40.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.969][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.970][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:40.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:40.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.971][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:40.972][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:40.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.972][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.973][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:40.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:40.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.974][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:40.975][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:40.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.975][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.976][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:40.976][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:40.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.977][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.977][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:40.978][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:40.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.978][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.979][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:40.979][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.980][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.980][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:40.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:40.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.982][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.982][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.983][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:40.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.985][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:40.985][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:40.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.986][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:40.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:40.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.988][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:40.989][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:40.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.989][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.990][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:40.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:40.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.992][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:40.992][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:40.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.993][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:40.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:40.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:40.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:40.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:40.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:41.018][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-07-08 12:46:41.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:41.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:41.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:41.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:41.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:41.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:41.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:41.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:41.028][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-07-08 12:46:41.029][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:41.030][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-07-08 12:46:41.030][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:41.031][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:41.031][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:41.032][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:41.032][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:41.033][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:41.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:41.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:41.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:41.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:41.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:41.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:41.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:41.041][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-07-08 12:46:41.042][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:41.043][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-08 12:46:41.044][rule$waitAsNeeded] Wait 0.037075 second(s).
biodb.TRACE[2024-07-08 12:46:41.082][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-07-08 12:46:41.169][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-07-08 12:46:41.248][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:41.249][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-07-08 12:46:41.252][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-07-08 12:46:41.254][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-07-08 12:46:41.255][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:41.255][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:41.256][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:41.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:41.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:41.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:41.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:41.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:41.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:41.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:41.265][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.265][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.266][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.282][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:41.283][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:41.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.284][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.285][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:41.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:41.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.288][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:41.289][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:41.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.290][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.292][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:41.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:41.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.294][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:41.295][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:41.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.296][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:41.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:41.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.300][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:41.300][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:41.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.301][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:41.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:41.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.304][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:41.305][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:41.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.307][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.308][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:41.309][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.310][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.310][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:41.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.313][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:41.315][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:41.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.317][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:41.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:41.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.322][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:41.322][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:41.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.324][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:41.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:41.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.328][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:41.328][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:41.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.330][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.330][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:41.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:41.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.333][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:41.334][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:41.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.335][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.336][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:41.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:41.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:41.382][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-07-08 12:46:41.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:41.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:41.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:41.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:41.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:41.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:41.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:41.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:41.404][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-07-08 12:46:41.405][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:41.407][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-07-08 12:46:41.408][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:41.409][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:41.410][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:41.411][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:41.412][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:41.413][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:41.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:41.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:41.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:41.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:41.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:41.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:41.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:41.427][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-07-08 12:46:41.430][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:41.432][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-08 12:46:41.433][rule$waitAsNeeded] Wait 0.0276771 second(s).
biodb.TRACE[2024-07-08 12:46:41.480][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-07-08 12:46:41.635][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-07-08 12:46:41.708][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:41.711][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-07-08 12:46:41.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-07-08 12:46:41.718][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-07-08 12:46:41.720][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:41.722][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:41.723][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:41.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:41.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:41.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:41.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:41.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:41.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:41.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:41.737][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.738][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.740][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.745][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:41.746][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:41.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.747][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.749][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:41.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:41.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.768][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:41.769][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:41.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.772][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:41.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:41.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.777][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:41.778][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:41.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.780][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:41.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:41.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.784][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:41.785][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:41.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.787][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:41.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:41.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.791][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:41.792][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:41.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.794][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.796][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:41.797][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.798][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.800][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:41.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.803][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:41.804][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:41.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.805][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:41.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:41.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.810][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:41.811][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:41.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.812][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:41.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:41.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.817][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:41.818][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:41.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.819][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.820][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:41.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:41.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.824][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:41.825][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:41.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.826][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.828][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:41.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:41.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:41.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:41.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:41.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:41.871][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-07-08 12:46:41.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:41.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:41.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:41.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:41.884][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:41.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:41.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:41.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:41.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:41.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:41.893][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[2024-07-08 12:46:41.894][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-07-08 12:46:41.895][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:41.897][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-07-08 12:46:41.898][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:41.899][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:41.900][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:41.901][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:41.902][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:41.903][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:41.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:41.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:41.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:41.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:41.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:41.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:41.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:41.916][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-07-08 12:46:41.919][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:41.920][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:41.922][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-07-08 12:46:42.043][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-07-08 12:46:42.119][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:42.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-07-08 12:46:42.125][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-07-08 12:46:42.128][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-07-08 12:46:42.129][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:42.131][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:42.132][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:42.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:42.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:42.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:42.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:42.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:42.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:42.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:42.146][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.147][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.149][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.153][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:42.154][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:42.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.156][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.157][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:42.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:42.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.161][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:42.162][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:42.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.164][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.165][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:42.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:42.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.168][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:42.169][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:42.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.171][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:42.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:42.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.186][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.187][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.189][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.191][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.194][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:42.195][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:42.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.196][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.198][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:42.198][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.200][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.201][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:42.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.204][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.205][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.207][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.212][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:42.213][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:42.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.214][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:42.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:42.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.220][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:42.220][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:42.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.222][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.223][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:42.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:42.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.227][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:42.228][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:42.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.229][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.230][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:42.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:42.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:42.266][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-07-08 12:46:42.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:42.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:42.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:42.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:42.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:42.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:42.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:42.295][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[2024-07-08 12:46:42.296][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-07-08 12:46:42.297][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:42.299][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-07-08 12:46:42.300][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:42.301][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:42.303][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:42.303][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:42.304][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:42.305][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:42.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:42.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:42.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:42.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:42.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:42.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:42.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:42.320][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-07-08 12:46:42.324][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:42.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:42.327][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-07-08 12:46:42.408][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-07-08 12:46:42.484][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:42.486][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-07-08 12:46:42.491][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-07-08 12:46:42.494][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-07-08 12:46:42.496][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:42.497][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:42.498][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:42.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:42.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:42.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:42.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:42.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:42.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:42.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:42.512][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.513][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.514][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.519][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:42.520][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:42.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.521][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.522][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:42.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:42.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.526][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:42.527][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:42.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.529][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.530][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:42.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:42.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.533][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:42.534][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:42.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.536][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:42.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:42.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.541][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.541][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.543][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.547][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:42.548][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:42.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.550][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.551][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:42.559][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.565][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.567][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:42.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.571][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.572][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.573][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.578][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:42.579][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:42.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.581][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:42.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:42.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.586][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:42.586][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:42.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.588][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.589][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:42.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:42.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.593][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:42.594][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:42.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.595][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:42.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:42.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:42.639][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-07-08 12:46:42.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:42.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:42.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:42.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:42.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:42.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:42.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:42.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:42.661][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-07-08 12:46:42.662][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:42.663][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-07-08 12:46:42.664][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:42.665][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:42.674][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:42.675][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:42.677][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:42.678][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:42.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:42.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:42.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:42.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:42.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:42.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:42.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:42.693][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-07-08 12:46:42.696][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:42.697][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:42.699][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-07-08 12:46:42.777][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-07-08 12:46:42.852][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:42.855][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-07-08 12:46:42.859][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-07-08 12:46:42.861][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-07-08 12:46:42.864][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:42.865][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:42.866][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:42.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:42.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:42.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:42.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:42.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:42.877][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:42.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:42.881][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.882][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.883][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.888][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:42.889][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:42.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.891][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.892][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:42.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:42.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.895][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:42.896][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:42.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.898][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.899][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:42.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:42.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.902][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:42.903][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:42.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.905][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.906][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:42.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:42.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.909][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.910][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.912][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:42.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.917][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:42.918][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:42.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.919][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.921][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:42.922][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.923][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.925][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:42.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:42.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.929][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.930][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.932][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:42.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.949][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:42.950][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:42.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.953][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:42.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:42.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.958][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:42.959][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:42.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.960][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.961][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:42.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:42.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.965][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:42.966][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:42.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.967][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.968][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:42.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:42.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:42.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:42.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:42.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:42.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:42.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.004][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-07-08 12:46:43.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:43.026][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-07-08 12:46:43.027][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:43.029][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-07-08 12:46:43.030][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:43.031][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:43.032][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:43.033][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:43.034][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:43.034][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:43.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:43.058][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-07-08 12:46:43.062][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:43.063][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:43.064][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-07-08 12:46:43.142][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-07-08 12:46:43.217][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:43.220][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-07-08 12:46:43.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-07-08 12:46:43.226][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-07-08 12:46:43.228][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:43.229][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:43.230][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:43.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:43.244][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.245][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.246][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.251][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:43.252][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:43.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.254][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.255][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:43.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:43.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.258][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:43.259][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:43.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.260][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.262][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:43.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:43.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.265][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:43.266][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:43.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.268][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:43.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:43.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.272][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:43.273][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:43.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.274][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:43.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:43.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.279][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:43.280][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:43.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.281][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.282][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:43.283][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.285][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.286][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:43.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.289][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:43.290][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:43.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.292][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:43.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:43.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.296][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:43.297][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:43.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.298][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:43.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:43.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.303][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:43.304][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:43.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.305][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.316][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:43.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:43.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.321][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:43.322][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:43.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.323][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.325][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:43.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:43.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.363][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-07-08 12:46:43.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:43.386][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-07-08 12:46:43.387][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:43.389][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-07-08 12:46:43.390][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:43.391][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:43.392][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:43.393][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:43.394][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:43.394][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:43.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:43.409][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-07-08 12:46:43.412][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:43.413][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:43.415][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-07-08 12:46:43.494][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-07-08 12:46:43.568][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:43.580][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-07-08 12:46:43.585][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-07-08 12:46:43.589][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-07-08 12:46:43.590][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:43.591][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:43.593][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:43.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:43.606][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.607][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.609][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.613][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:43.614][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:43.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.616][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.617][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:43.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:43.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.620][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:43.621][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:43.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.623][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.624][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:43.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:43.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.627][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:43.628][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:43.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.630][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:43.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:43.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.634][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:43.635][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:43.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.636][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:43.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:43.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.641][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:43.641][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:43.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.643][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.644][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:43.645][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.647][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.649][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:43.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.653][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:43.654][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:43.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.655][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:43.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:43.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.660][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:43.661][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:43.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.663][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.664][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:43.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:43.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.668][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:43.669][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:43.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.670][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.671][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:43.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:43.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.675][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:43.676][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:43.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.677][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.679][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:43.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:43.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:43.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:43.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:43.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.727][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-07-08 12:46:43.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.759][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:43.763][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:43.764][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-08 12:46:43.765][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:43.767][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-08 12:46:43.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:43.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.809][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[2024-07-08 12:46:43.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:43.842][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.868][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.TRACE[2024-07-08 12:46:43.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:43.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:43.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.960][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.TRACE[2024-07-08 12:46:43.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:43.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:43.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:43.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:43.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:43.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:43.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:43.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:43.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:43.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:43.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:43.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:44.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.023][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.TRACE[2024-07-08 12:46:44.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.042][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:44.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.058][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:44.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:44.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:44.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:44.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.168][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.TRACE[2024-07-08 12:46:44.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:44.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:44.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:44.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.255][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[2024-07-08 12:46:44.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:44.337][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:44.340][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:44.341][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:44.343][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:44.420][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:44.492][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:44.494][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-07-08 12:46:44.499][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-07-08 12:46:44.503][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:44.507][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:44.508][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:44.510][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:44.586][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:44.660][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:44.663][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-07-08 12:46:44.668][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-07-08 12:46:44.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:44.698][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-07-08 12:46:44.699][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:44.700][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-07-08 12:46:44.702][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:44.703][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:44.704][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:44.705][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:44.706][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:44.706][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:44.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:44.721][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-07-08 12:46:44.724][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:44.725][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:44.727][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-07-08 12:46:44.808][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-07-08 12:46:44.891][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:44.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-07-08 12:46:44.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-07-08 12:46:44.901][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-07-08 12:46:44.903][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:44.904][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:44.905][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:44.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:44.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:44.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:44.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:44.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:44.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:44.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:44.919][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:44.920][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:44.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.921][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:44.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:44.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.926][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:44.927][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:44.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.928][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.930][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:44.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:44.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.933][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:44.934][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:44.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.935][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.937][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:44.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:44.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.940][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:44.941][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:44.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.942][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.944][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:44.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:44.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.947][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:44.948][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:44.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.949][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:44.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:44.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.954][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:44.955][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:44.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.968][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.970][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:44.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:44.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.974][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:44.975][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.977][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.978][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:44.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:44.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.982][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.982][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.984][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:44.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.989][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:44.990][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:44.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.991][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:44.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:44.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:44.996][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:44.997][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:44.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:44.999][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.000][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:45.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:45.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.004][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:45.004][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:45.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.006][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.007][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:45.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:45.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:45.046][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-07-08 12:46:45.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:45.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:45.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:45.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:45.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:45.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:45.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:45.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:45.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:45.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:45.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:45.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:45.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:45.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:45.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:45.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:45.097][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-07-08 12:46:45.098][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:45.100][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-07-08 12:46:45.101][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:45.102][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:45.103][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:45.104][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:45.105][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:45.106][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:45.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:45.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:45.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:45.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:45.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:45.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:45.119][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.DEBUG[2024-07-08 12:46:45.120][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-07-08 12:46:45.124][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:45.125][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-08 12:46:45.127][rule$waitAsNeeded] Wait 0.215943 second(s).
biodb.TRACE[2024-07-08 12:46:45.495][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-07-08 12:46:45.589][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-07-08 12:46:45.669][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:45.672][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-07-08 12:46:45.677][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-07-08 12:46:45.681][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-07-08 12:46:45.683][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:45.684][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:45.685][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:45.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:45.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:45.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:45.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:45.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:45.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:45.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:45.703][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.704][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.706][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.713][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:45.714][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:45.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.717][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.718][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:45.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:45.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.722][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:45.723][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:45.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.724][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.725][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:45.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:45.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.729][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:45.737][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:45.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.743][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:45.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:45.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.749][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:45.750][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:45.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.752][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:45.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:45.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.756][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:45.757][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:45.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.759][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.760][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:45.761][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:45.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.763][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.764][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:45.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:45.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.768][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.768][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.770][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.775][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:45.775][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:45.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.777][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:45.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:45.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.782][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:45.782][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:45.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.784][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.785][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:45.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:45.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.790][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:45.791][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:45.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.793][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.794][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:45.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:45.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:45.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:45.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:45.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:45.834][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-07-08 12:46:45.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:45.876][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:45.879][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:45.881][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-08 12:46:45.882][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:45.884][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-08 12:46:45.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:45.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:45.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:45.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:45.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:45.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:45.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:45.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:45.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:45.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:45.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:45.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:45.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:45.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:45.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:45.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:45.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:45.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:45.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:45.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:45.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:45.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:45.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:45.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:45.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:45.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:45.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.201][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.410][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.459][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.603][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:46.607][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:46.609][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-08 12:46:46.610][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:46.611][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-08 12:46:46.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:46.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:46.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:46.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:46.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:46.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:46.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:46.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:46.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:46.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:46.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:46.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.085][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-08 12:46:47.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-08 12:46:47.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 12:46:47.097][biodb::testThat]
biodb.INFO [2024-07-08 12:46:47.098][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-07-08 12:46:47.099][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:47.100][biodb::testThat]
biodb.TRACE[2024-07-08 12:46:47.103][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-08 12:46:47.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-08 12:46:47.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:47.136][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:47.140][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:47.141][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-08 12:46:47.143][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:47.144][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-08 12:46:47.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.168][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:47.172][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:47.173][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-08 12:46:47.174][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:47.175][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-08 12:46:47.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:47.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.219][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-08 12:46:47.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.245][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.246][private$selectFields]
biodb.TRACE[2024-07-08 12:46:47.247][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:47.247][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:47.248][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.249][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.250][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.251][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.252][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.253][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.254][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.255][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.256][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.257][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.257][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.259][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.260][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:47.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.280][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-08 12:46:47.281][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.298][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.299][private$selectFields]
biodb.TRACE[2024-07-08 12:46:47.300][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:47.301][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:47.301][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.302][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.303][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.305][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.306][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.308][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.308][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.309][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.310][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.311][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.312][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.313][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:47.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.324][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-08 12:46:47.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.343][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.343][private$selectFields]
biodb.TRACE[2024-07-08 12:46:47.344][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:47.345][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:47.346][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.346][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.347][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.349][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.350][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.350][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.352][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.353][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.354][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:47.354][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.355][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.357][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.358][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:47.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.368][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-08 12:46:47.369][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-08 12:46:47.370][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-08 12:46:47.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:47.466][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:47.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:47.471][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:47.473][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:47.603][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:47.684][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:47.687][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-07-08 12:46:47.691][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-07-08 12:46:47.696][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:47.699][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:47.700][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:47.702][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:47.778][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:47.849][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:47.852][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-07-08 12:46:47.856][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-07-08 12:46:47.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:47.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:47.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:47.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:47.961][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-08 12:46:47.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:47.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:47.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:47.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:47.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:47.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:47.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:47.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:47.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.005][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.005][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.006][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.007][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.008][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.009][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.010][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.011][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.015][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.016][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.017][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.018][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.019][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.020][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.021][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.032][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-08 12:46:48.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.084][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.085][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.086][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.087][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.088][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.089][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.090][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.091][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.092][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.093][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.094][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.095][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.105][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.106][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.107][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.109][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.110][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.121][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-08 12:46:48.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.139][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.140][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.141][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.141][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.142][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.143][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.144][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.145][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.146][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.147][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.148][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.149][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.150][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.151][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.152][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.154][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.154][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.166][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-08 12:46:48.167][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-08 12:46:48.167][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-08 12:46:48.177][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-08 12:46:48.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-08 12:46:48.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 12:46:48.185][biodb::testThat]
biodb.INFO [2024-07-08 12:46:48.186][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-07-08 12:46:48.187][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:48.187][biodb::testThat]
biodb.TRACE[2024-07-08 12:46:48.191][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-08 12:46:48.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-08 12:46:48.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:48.231][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:48.234][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:48.236][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-08 12:46:48.237][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:48.239][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-08 12:46:48.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.264][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:48.267][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:48.268][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-08 12:46:48.270][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:48.271][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-08 12:46:48.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.314][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-08 12:46:48.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.324][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.333][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.333][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.334][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.335][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.336][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.337][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.338][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.339][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.340][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.342][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.343][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.344][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.345][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.346][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.347][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.348][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.360][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-08 12:46:48.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.379][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.380][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.381][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.381][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.382][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.383][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.384][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.386][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.387][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.388][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.390][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.391][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.391][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.392][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.393][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.395][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.396][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.408][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-08 12:46:48.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.426][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.427][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.428][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.429][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.429][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.430][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.431][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.433][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.434][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.435][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.436][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.437][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.438][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.438][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.439][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.441][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.442][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.454][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-08 12:46:48.455][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-08 12:46:48.455][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-08 12:46:48.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:48.495][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:48.498][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:48.499][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-07-08 12:46:48.501][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:48.502][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-07-08 12:46:48.505][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:48.509][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:48.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-07-08 12:46:48.512][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:48.514][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-07-08 12:46:48.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.554][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:48.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.589][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-08 12:46:48.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.608][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.609][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.610][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.610][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.611][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.612][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.613][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.614][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.615][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.616][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.617][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.618][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.619][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.620][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.620][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.622][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.623][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.633][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-08 12:46:48.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.643][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[2024-07-08 12:46:48.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.651][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.652][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.653][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.654][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.654][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.655][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.656][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.658][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.658][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.659][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.661][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.662][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.663][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.663][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.664][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.666][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.667][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.678][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-08 12:46:48.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.696][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.697][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.697][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.698][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.699][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.700][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.701][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.703][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.703][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.704][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.706][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.707][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.707][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.708][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.709][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.711][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.711][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.722][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-08 12:46:48.723][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-08 12:46:48.724][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-08 12:46:48.733][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-08 12:46:48.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-08 12:46:48.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 12:46:48.740][biodb::testThat]
biodb.INFO [2024-07-08 12:46:48.741][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-07-08 12:46:48.742][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:48.743][biodb::testThat]
biodb.TRACE[2024-07-08 12:46:48.746][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-08 12:46:48.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-08 12:46:48.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.777][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:48.780][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:48.784][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:48.785][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-08 12:46:48.787][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:48.788][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-08 12:46:48.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.814][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:48.817][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:48.818][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-08 12:46:48.819][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:48.821][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-08 12:46:48.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:48.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:48.864][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-08 12:46:48.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.891][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.892][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.893][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.893][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.894][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.895][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.896][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.898][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.898][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.899][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.901][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.902][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.903][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.904][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.905][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.906][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.907][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.918][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-08 12:46:48.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.937][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.938][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.939][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.940][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.941][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.942][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.943][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.944][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.945][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.946][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.948][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.948][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.949][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.950][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.951][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.954][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.954][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:48.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.965][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-08 12:46:48.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:48.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:48.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:48.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:48.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:48.975][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:48.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:48.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.984][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.985][private$selectFields]
biodb.TRACE[2024-07-08 12:46:48.986][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:48.987][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:48.988][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.989][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.990][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.991][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.992][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.993][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:48.995][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:48.996][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.997][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:48.998][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:48.999][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.001][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.002][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:49.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.013][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-08 12:46:49.014][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-08 12:46:49.015][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-08 12:46:49.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:49.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:49.071][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:49.074][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:49.076][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-07-08 12:46:49.078][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:49.079][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-07-08 12:46:49.083][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:49.087][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:49.088][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-07-08 12:46:49.090][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:49.091][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-07-08 12:46:49.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:49.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:49.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:49.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:49.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:49.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:49.159][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-08 12:46:49.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:49.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.177][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.178][private$selectFields]
biodb.TRACE[2024-07-08 12:46:49.179][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:49.180][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:49.181][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.181][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.182][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.184][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.184][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.185][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.187][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.188][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.188][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.189][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.190][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.192][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.192][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:49.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.203][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-08 12:46:49.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.220][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.TRACE[2024-07-08 12:46:49.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.228][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.228][private$selectFields]
biodb.TRACE[2024-07-08 12:46:49.229][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:49.230][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:49.231][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.232][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.233][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.234][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.235][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.236][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.237][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.238][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.239][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.240][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.241][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.242][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.243][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:49.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.253][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-08 12:46:49.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:49.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.271][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.272][private$selectFields]
biodb.TRACE[2024-07-08 12:46:49.272][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-08 12:46:49.273][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-08 12:46:49.274][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.275][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.275][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.277][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.278][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.278][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.280][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.281][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.282][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-08 12:46:49.282][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.283][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.285][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.285][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-08 12:46:49.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.296][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-08 12:46:49.297][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-08 12:46:49.298][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-08 12:46:49.317][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-08 12:46:49.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-08 12:46:49.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-08 12:46:49.324][biodb::testThat]
biodb.INFO [2024-07-08 12:46:49.325][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-07-08 12:46:49.326][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:49.327][biodb::testThat]
biodb.DEBUG[2024-07-08 12:46:49.329][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-07-08 12:46:49.330][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:49.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-07-08 12:46:49.332][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:49.333][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:49.334][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:49.335][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:49.336][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:49.337][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:49.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:49.350][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-07-08 12:46:49.352][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:49.353][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:49.355][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-07-08 12:46:49.434][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-07-08 12:46:49.505][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:49.508][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-07-08 12:46:49.512][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-07-08 12:46:49.515][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-07-08 12:46:49.517][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:49.518][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:49.519][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:49.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:49.534][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:49.535][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:49.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.537][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:49.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:49.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.542][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:49.543][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:49.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.544][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.545][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:49.546][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:49.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.548][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.549][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:49.550][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:49.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.552][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.553][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:49.554][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:49.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.555][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.556][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:49.557][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:49.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.559][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.560][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:49.561][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:49.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.563][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.565][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.566][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:49.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.568][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.569][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:49.570][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:49.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.571][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.573][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:49.573][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:49.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.575][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.576][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:49.577][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:49.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.578][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:49.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:49.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:49.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:49.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:49.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:49.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:49.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:49.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:49.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:49.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:49.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:49.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:49.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:49.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:49.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:49.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:49.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:49.612][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-07-08 12:46:49.613][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-07-08 12:46:49.621][biodb::testThat]
biodb.INFO [2024-07-08 12:46:49.623][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-07-08 12:46:49.623][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:49.624][biodb::testThat]
biodb.DEBUG[2024-07-08 12:46:49.634][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-07-08 12:46:49.636][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-07-08 12:46:49.637][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-07-08 12:46:49.638][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-07-08 12:46:49.640][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2024-07-08 12:46:49.641][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2024-07-08 12:46:49.642][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:49.643][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:49.644][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:49.645][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:49.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:49.659][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-07-08 12:46:49.662][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:49.663][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:49.664][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-07-08 12:46:49.747][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-07-08 12:46:49.823][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:49.825][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-07-08 12:46:49.829][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-07-08 12:46:49.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:49.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:49.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:49.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:49.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:49.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:49.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:49.854][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-07-08 12:46:49.857][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:49.858][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:49.859][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-07-08 12:46:49.951][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-07-08 12:46:50.040][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:50.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-07-08 12:46:50.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-07-08 12:46:50.050][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-07-08 12:46:50.052][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:50.053][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-07-08 12:46:50.055][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:50.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:50.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:50.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:50.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:50.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:50.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:50.069][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.070][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.072][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.077][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:50.078][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:50.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.079][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.080][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:50.081][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:50.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.083][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.084][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:50.085][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:50.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.087][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.088][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:50.089][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:50.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.090][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.091][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:50.092][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:50.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.094][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.095][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:50.096][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:50.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.097][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.098][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.099][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.101][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.102][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:50.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:50.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.105][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.106][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:50.107][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:50.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.108][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.109][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:50.110][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:50.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.112][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:50.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:50.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:50.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:50.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:50.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:50.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.146][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.TRACE[2024-07-08 12:46:50.149][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.150][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.152][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.156][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:50.157][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:50.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.159][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.160][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:50.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:50.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.164][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:50.165][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:50.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.167][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.168][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:50.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:50.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.172][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:50.173][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:50.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.174][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.175][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:50.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:50.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.179][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:50.179][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:50.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.181][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.182][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:50.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:50.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.185][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:50.186][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:50.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.188][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.189][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:50.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:50.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.192][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:50.193][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:50.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.195][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.196][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:50.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:50.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.200][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.201][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.202][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.207][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:50.208][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:50.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.210][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.211][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:50.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:50.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.214][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:50.215][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:50.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.218][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.220][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:50.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:50.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.224][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:50.225][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:50.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.227][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.229][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:50.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:50.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:50.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:50.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:50.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:50.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:50.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:50.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:50.295][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.296][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.298][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.303][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:50.304][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:50.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.305][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.306][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:50.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:50.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.310][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:50.311][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:50.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.312][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.313][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:50.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:50.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.317][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:50.318][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:50.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.319][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:50.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:50.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.324][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:50.324][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:50.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.326][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.327][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:50.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:50.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.330][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:50.331][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:50.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.333][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.334][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:50.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:50.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.337][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:50.338][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:50.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.340][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.341][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:50.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:50.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.345][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.346][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.347][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.352][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:50.353][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:50.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.354][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:50.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:50.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.359][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:50.360][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:50.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.361][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.363][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:50.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:50.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.372][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:50.377][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:50.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.378][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.380][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:50.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:50.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:50.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:50.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:50.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:50.437][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-07-08 12:46:50.437][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-08 12:46:50.438][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-07-08 12:46:50.453][biodb::testThat]
biodb.INFO [2024-07-08 12:46:50.454][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-07-08 12:46:50.455][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:50.455][biodb::testThat]
biodb.INFO [2024-07-08 12:46:50.481][biodb::testThat]
biodb.INFO [2024-07-08 12:46:50.482][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-07-08 12:46:50.483][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:50.484][biodb::testThat]
biodb.INFO [2024-07-08 12:46:50.493][biodb::testThat]
biodb.INFO [2024-07-08 12:46:50.494][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-07-08 12:46:50.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:50.496][biodb::testThat]
biodb.DEBUG[2024-07-08 12:46:50.499][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:50.502][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:50.503][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:50.505][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:50.663][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:50.838][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:50.840][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-07-08 12:46:50.845][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-07-08 12:46:50.858][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:50.860][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:50.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.862][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:50.863][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.863][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:50.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:50.865][ef$get] fields variable is a list.
biodb.INFO [2024-07-08 12:46:50.867][biodb::testThat]
biodb.INFO [2024-07-08 12:46:50.868][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-07-08 12:46:50.868][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:50.869][biodb::testThat]
biodb.ERROR[2024-07-08 12:46:50.885][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-07-08 12:46:50.903][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-07-08 12:46:50.917][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-08 12:46:50.919][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-08 12:46:50.920][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-08 12:46:50.921][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-08 12:46:50.921][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:50.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:50.923][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:50.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:50.924][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-08 12:46:50.936][biodb::testContext]
biodb.INFO [2024-07-08 12:46:50.937][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 12:46:50.938][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-07-08 12:46:50.939][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 12:46:50.940][biodb::testContext]
biodb.INFO [2024-07-08 12:46:50.942][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-08 12:46:50.945][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-08 12:46:50.950][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:50.952][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-08 12:46:50.953][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-08 12:46:50.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:50.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:50.956][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-08 12:46:50.957][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-08 12:46:50.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:50.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:50.960][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-08 12:46:50.961][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-08 12:46:50.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:50.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.963][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[2024-07-08 12:46:50.964][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-08 12:46:50.965][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-08 12:46:50.966][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-08 12:46:50.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:50.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:50.969][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-08 12:46:50.970][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-08 12:46:50.971][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-08 12:46:50.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:50.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.973][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[2024-07-08 12:46:50.974][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-08 12:46:50.975][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-08 12:46:50.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:50.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:50.978][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-08 12:46:50.979][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-08 12:46:50.980][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-08 12:46:50.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:50.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:50.983][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-08 12:46:50.984][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-08 12:46:50.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:50.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:50.987][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-08 12:46:50.987][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-08 12:46:50.988][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-08 12:46:50.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:50.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:50.991][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-08 12:46:50.992][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-08 12:46:50.993][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-08 12:46:50.995][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-08 12:46:50.995][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-08 12:46:50.996][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-08 12:46:50.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:50.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:50.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:50.999][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-08 12:46:51.000][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-08 12:46:51.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.003][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-08 12:46:51.004][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-08 12:46:51.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.007][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-08 12:46:51.008][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-08 12:46:51.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.011][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-08 12:46:51.011][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-08 12:46:51.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.014][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-08 12:46:51.015][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-08 12:46:51.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.018][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-08 12:46:51.019][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-08 12:46:51.035][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-08 12:46:51.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.039][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-08 12:46:51.040][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-08 12:46:51.041][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-08 12:46:51.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.044][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-08 12:46:51.045][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.046][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-08 12:46:51.047][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.055][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:51.060][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.061][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.061][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.062][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.063][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 12:46:51.064][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:51.065][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.065][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-08 12:46:51.066][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:51.067][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.068][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.069][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:51.069][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:51.069][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:51.069][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 12:46:51.069][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 12:46:51.070][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:51.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:51.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:51.072][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:51.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:51.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:51.074][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.075][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.076][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:51.077][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:51.077][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.078][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.079][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-08 12:46:51.081][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.082][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 12:46:51.083][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.084][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:51.085][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.086][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.087][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.087][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.088][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 12:46:51.089][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:51.090][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.091][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-08 12:46:51.091][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:51.092][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.093][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.094][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:51.094][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:51.094][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:51.094][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 12:46:51.094][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 12:46:51.095][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:51.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:51.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:51.097][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:51.098][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:51.098][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:51.099][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.100][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.101][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:51.101][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:51.102][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.103][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.104][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-08 12:46:51.105][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.106][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-08 12:46:51.107][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.108][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:51.109][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.110][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.110][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.111][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.112][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 12:46:51.113][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:51.113][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.114][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-08 12:46:51.115][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:51.116][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.117][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.117][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.118][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:51.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:51.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:51.121][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:51.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:51.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:51.123][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.124][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.124][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:51.125][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:51.126][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.127][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.128][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-08 12:46:51.129][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.130][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 12:46:51.131][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.132][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:51.133][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.133][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.134][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.135][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.136][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 12:46:51.136][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:51.137][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.138][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-08 12:46:51.139][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:51.140][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.141][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.141][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.142][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:51.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:51.143][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:51.144][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:51.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:51.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:51.146][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.147][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.148][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:51.149][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:51.150][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.150][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:51.151][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:51.152][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.153][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[2024-07-08 12:46:51.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.160][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[2024-07-08 12:46:51.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.214][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-08 12:46:51.215][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-08 12:46:51.216][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-08 12:46:51.218][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-08 12:46:51.219][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 12:46:51.220][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-08 12:46:51.221][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-08 12:46:51.223][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-08 12:46:51.224][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-08 12:46:51.225][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-08 12:46:51.226][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 12:46:51.228][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-08 12:46:51.229][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-08 12:46:51.230][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-08 12:46:51.231][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-08 12:46:51.233][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-08 12:46:51.234][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-08 12:46:51.235][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-08 12:46:51.236][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 12:46:51.237][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-08 12:46:51.238][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-08 12:46:51.240][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-08 12:46:51.241][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-08 12:46:51.243][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-08 12:46:51.244][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-08 12:46:51.246][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-08 12:46:51.247][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-08 12:46:51.248][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-08 12:46:51.249][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-08 12:46:51.251][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-08 12:46:51.252][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-08 12:46:51.253][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-08 12:46:51.254][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-08 12:46:51.255][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-08 12:46:51.256][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-08 12:46:51.257][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-08 12:46:51.259][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-08 12:46:51.260][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-08 12:46:51.261][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-08 12:46:51.262][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-08 12:46:51.263][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-08 12:46:51.264][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-08 12:46:51.265][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-08 12:46:51.267][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-08 12:46:51.268][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-08 12:46:51.269][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-08 12:46:51.270][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-08 12:46:51.271][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-08 12:46:51.272][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-08 12:46:51.274][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-08 12:46:51.275][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-08 12:46:51.276][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-08 12:46:51.277][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-08 12:46:51.278][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-08 12:46:51.280][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-08 12:46:51.281][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-08 12:46:51.282][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-08 12:46:51.283][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-08 12:46:51.284][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-08 12:46:51.285][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-08 12:46:51.286][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-08 12:46:51.287][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-08 12:46:51.288][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-08 12:46:51.290][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-08 12:46:51.291][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-08 12:46:51.292][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-08 12:46:51.293][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 12:46:51.294][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 12:46:51.295][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-08 12:46:51.296][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-08 12:46:51.298][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-08 12:46:51.299][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-08 12:46:51.300][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-08 12:46:51.301][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-08 12:46:51.302][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-08 12:46:51.303][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-08 12:46:51.304][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-08 12:46:51.306][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-08 12:46:51.307][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-08 12:46:51.308][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-08 12:46:51.309][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-08 12:46:51.310][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-08 12:46:51.311][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-08 12:46:51.312][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-08 12:46:51.314][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-08 12:46:51.315][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:51.316][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.318][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.323][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[2024-07-08 12:46:51.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.382][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.DEBUG[2024-07-08 12:46:51.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:51.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.414][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-08 12:46:51.416][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-08 12:46:51.418][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.419][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.420][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.421][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:51.422][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.423][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.423][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.424][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-08 12:46:51.425][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-08 12:46:51.426][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:51.427][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.428][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-08 12:46:51.429][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-08 12:46:51.430][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-08 12:46:51.431][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:51.431][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:51.431][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:51.431][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:51.432][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-08 12:46:51.433][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:51.434][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:51.435][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:51.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:51.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:51.437][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:51.438][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:51.438][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-08 12:46:51.439][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:51.440][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:51.440][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:51.441][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-08 12:46:51.441][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-08 12:46:51.442][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 12:46:51.444][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 12:46:51.445][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-08 12:46:51.446][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 12:46:51.448][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 12:46:51.449][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 12:46:51.452][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-08 12:46:51.453][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-08 12:46:51.454][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-08 12:46:51.456][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-08 12:46:51.457][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-08 12:46:51.458][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-08 12:46:51.459][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-08 12:46:51.460][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-08 12:46:51.461][biodb::testThat]
biodb.INFO [2024-07-08 12:46:51.462][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-07-08 12:46:51.463][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:51.463][biodb::testThat]
biodb.DEBUG[2024-07-08 12:46:51.467][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-08 12:46:51.471][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:51.473][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-08 12:46:51.474][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:51.476][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-08 12:46:51.480][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:51.485][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:51.487][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-08 12:46:51.488][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:51.490][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-08 12:46:51.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:51.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.506][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:51.510][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:51.512][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-08 12:46:51.513][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:51.515][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-08 12:46:51.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:51.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.528][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.DEBUG[2024-07-08 12:46:51.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:51.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.563][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:51.566][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:51.568][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-08 12:46:51.569][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:51.570][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-08 12:46:51.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:51.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.583][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:51.586][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:51.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-08 12:46:51.589][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:51.590][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-08 12:46:51.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:51.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:51.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.616][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:51.620][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:51.621][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-08 12:46:51.622][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:51.624][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-08 12:46:51.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:51.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.634][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.637][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:51.640][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:51.641][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-08 12:46:51.643][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:51.644][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-08 12:46:51.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:51.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.657][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:51.661][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:51.662][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-07-08 12:46:51.663][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:51.666][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-07-08 12:46:51.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:51.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-08 12:46:51.694][biodb::testThat]
biodb.INFO [2024-07-08 12:46:51.695][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-07-08 12:46:51.696][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:51.697][biodb::testThat]
biodb.DEBUG[2024-07-08 12:46:51.701][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:51.705][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:51.706][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:51.708][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:51.833][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:51.904][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:51.907][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-07-08 12:46:51.911][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-07-08 12:46:51.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:51.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:51.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:51.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:51.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:51.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:51.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:51.927][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:51.931][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:51.932][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:51.933][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:52.010][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:52.099][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:52.102][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-07-08 12:46:52.106][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-07-08 12:46:52.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:52.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-08 12:46:52.124][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-08 12:46:52.125][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-08 12:46:52.126][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-08 12:46:52.127][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-08 12:46:52.128][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.129][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.131][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-08 12:46:52.136][biodb::testContext]
biodb.INFO [2024-07-08 12:46:52.137][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 12:46:52.138][biodb::testContext] Test context - Test web services
biodb.INFO [2024-07-08 12:46:52.138][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 12:46:52.139][biodb::testContext]
biodb.INFO [2024-07-08 12:46:52.142][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-08 12:46:52.143][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-08 12:46:52.149][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:52.150][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-08 12:46:52.151][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.153][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[2024-07-08 12:46:52.154][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-08 12:46:52.155][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.158][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-08 12:46:52.159][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.162][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[2024-07-08 12:46:52.162][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-08 12:46:52.163][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-08 12:46:52.164][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-08 12:46:52.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.167][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-08 12:46:52.168][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-08 12:46:52.169][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.172][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-08 12:46:52.173][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-08 12:46:52.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.176][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-08 12:46:52.177][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-08 12:46:52.177][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-08 12:46:52.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.180][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-08 12:46:52.181][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.184][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-08 12:46:52.185][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-08 12:46:52.186][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.188][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-08 12:46:52.189][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-08 12:46:52.190][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-08 12:46:52.191][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-08 12:46:52.192][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-08 12:46:52.193][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-08 12:46:52.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.196][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-08 12:46:52.196][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-08 12:46:52.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.199][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[2024-07-08 12:46:52.199][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-08 12:46:52.200][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-08 12:46:52.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.203][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-08 12:46:52.204][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-08 12:46:52.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.207][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-08 12:46:52.208][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-08 12:46:52.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.211][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-08 12:46:52.212][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-08 12:46:52.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.214][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[2024-07-08 12:46:52.215][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-08 12:46:52.216][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-08 12:46:52.233][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-08 12:46:52.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.237][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-08 12:46:52.238][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-08 12:46:52.239][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-08 12:46:52.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.242][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-08 12:46:52.244][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.245][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-08 12:46:52.246][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.247][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:52.248][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.249][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.249][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.250][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.251][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 12:46:52.252][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:52.253][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.254][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-08 12:46:52.254][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:52.255][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.256][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.257][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:52.257][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:52.257][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:52.257][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 12:46:52.257][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 12:46:52.258][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:52.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:52.259][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:52.260][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:52.261][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:52.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:52.263][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.263][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.264][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:52.265][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:52.266][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.267][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.268][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-08 12:46:52.269][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.270][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 12:46:52.271][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.272][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:52.273][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.273][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.274][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.275][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.276][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 12:46:52.277][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:52.278][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.278][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-08 12:46:52.279][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:52.280][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.281][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.282][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:52.282][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:52.282][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:52.282][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 12:46:52.282][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 12:46:52.283][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:52.284][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:52.285][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:52.286][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:52.287][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:52.288][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:52.289][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.290][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.291][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:52.292][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:52.293][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.294][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.296][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-08 12:46:52.298][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.299][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-08 12:46:52.301][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.302][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:52.303][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.304][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.306][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.307][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.308][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 12:46:52.310][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:52.311][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.311][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-08 12:46:52.312][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:52.313][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.314][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.315][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.316][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:52.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:52.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:52.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:52.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:52.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:52.320][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.321][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:52.323][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:52.323][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.324][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.325][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-08 12:46:52.327][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.328][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 12:46:52.329][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.330][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:52.331][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.332][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.333][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.333][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.334][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 12:46:52.335][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:52.336][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.337][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-08 12:46:52.338][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:52.338][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.339][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.340][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.341][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:52.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:52.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:52.343][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:52.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:52.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:52.345][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.346][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.347][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:52.348][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:52.349][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.350][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:52.352][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:52.353][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.431][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-08 12:46:52.433][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-08 12:46:52.434][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-08 12:46:52.435][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-08 12:46:52.436][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 12:46:52.438][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-08 12:46:52.439][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-08 12:46:52.440][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-08 12:46:52.441][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-08 12:46:52.442][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-08 12:46:52.444][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 12:46:52.445][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-08 12:46:52.446][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-08 12:46:52.447][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-08 12:46:52.448][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-08 12:46:52.450][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-08 12:46:52.451][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-08 12:46:52.452][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-08 12:46:52.454][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 12:46:52.455][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-08 12:46:52.456][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-08 12:46:52.458][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-08 12:46:52.459][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-08 12:46:52.460][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-08 12:46:52.461][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-08 12:46:52.462][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-08 12:46:52.464][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-08 12:46:52.465][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-08 12:46:52.466][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-08 12:46:52.467][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-08 12:46:52.469][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-08 12:46:52.470][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-08 12:46:52.471][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-08 12:46:52.472][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-08 12:46:52.474][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-08 12:46:52.475][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-08 12:46:52.476][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-08 12:46:52.477][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-08 12:46:52.478][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-08 12:46:52.479][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-08 12:46:52.481][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-08 12:46:52.482][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-08 12:46:52.483][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-08 12:46:52.484][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-08 12:46:52.485][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-08 12:46:52.487][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-08 12:46:52.488][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-08 12:46:52.489][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-08 12:46:52.490][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-08 12:46:52.491][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-08 12:46:52.492][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-08 12:46:52.493][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-08 12:46:52.495][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-08 12:46:52.496][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-08 12:46:52.497][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-08 12:46:52.498][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-08 12:46:52.500][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-08 12:46:52.501][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-08 12:46:52.502][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-08 12:46:52.504][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-08 12:46:52.505][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-08 12:46:52.506][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-08 12:46:52.508][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-08 12:46:52.509][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-08 12:46:52.510][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-08 12:46:52.512][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-08 12:46:52.513][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 12:46:52.515][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 12:46:52.516][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-08 12:46:52.518][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-08 12:46:52.519][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-08 12:46:52.520][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-08 12:46:52.521][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-08 12:46:52.523][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-08 12:46:52.524][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-08 12:46:52.526][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-08 12:46:52.527][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-08 12:46:52.529][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-08 12:46:52.531][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-08 12:46:52.532][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-08 12:46:52.534][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-08 12:46:52.535][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-08 12:46:52.536][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-08 12:46:52.537][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-08 12:46:52.539][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-08 12:46:52.540][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:52.541][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.542][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.573][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[2024-07-08 12:46:52.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.630][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-08 12:46:52.632][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-08 12:46:52.634][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.635][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.636][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.636][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:52.637][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.638][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.639][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.640][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-08 12:46:52.641][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-08 12:46:52.641][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:52.642][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.643][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-08 12:46:52.644][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-08 12:46:52.645][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-08 12:46:52.646][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:52.647][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:52.647][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:52.647][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:52.647][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-08 12:46:52.648][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:52.649][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:52.650][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:52.651][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:52.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:52.652][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:52.653][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:52.653][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-08 12:46:52.654][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:52.654][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:52.655][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:52.656][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-08 12:46:52.656][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-08 12:46:52.657][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 12:46:52.659][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 12:46:52.668][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-08 12:46:52.670][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 12:46:52.671][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 12:46:52.672][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 12:46:52.676][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-08 12:46:52.677][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-08 12:46:52.678][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-08 12:46:52.679][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-08 12:46:52.680][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-08 12:46:52.681][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-08 12:46:52.682][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-08 12:46:52.683][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-08 12:46:52.684][biodb::testThat]
biodb.INFO [2024-07-08 12:46:52.685][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-07-08 12:46:52.686][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:52.686][biodb::testThat]
biodb.DEBUG[2024-07-08 12:46:52.690][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-08 12:46:52.693][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:52.695][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-08 12:46:52.696][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:52.697][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-08 12:46:52.701][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:52.705][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:52.706][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:52.707][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-08 12:46:52.786][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-08 12:46:52.873][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:52.876][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-07-08 12:46:52.880][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-07-08 12:46:52.890][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-08 12:46:52.892][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-08 12:46:52.893][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-08 12:46:52.894][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-08 12:46:52.895][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:52.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:52.896][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:52.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:52.898][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.898][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.INFO [2024-07-08 12:46:52.902][biodb::testContext]
biodb.INFO [2024-07-08 12:46:52.903][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 12:46:52.904][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-07-08 12:46:52.905][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-08 12:46:52.906][biodb::testContext]
biodb.INFO [2024-07-08 12:46:52.908][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-08 12:46:52.910][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-08 12:46:52.915][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:52.916][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-08 12:46:52.917][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.921][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-08 12:46:52.922][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.925][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-08 12:46:52.926][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.928][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-08 12:46:52.929][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-08 12:46:52.930][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-08 12:46:52.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.933][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-08 12:46:52.934][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-08 12:46:52.935][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.938][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-08 12:46:52.939][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-08 12:46:52.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.942][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-08 12:46:52.943][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-08 12:46:52.944][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-08 12:46:52.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.947][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-08 12:46:52.948][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.951][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-08 12:46:52.953][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-08 12:46:52.954][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-08 12:46:52.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.957][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-08 12:46:52.958][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-08 12:46:52.959][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-08 12:46:52.960][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-08 12:46:52.961][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-08 12:46:52.962][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-08 12:46:52.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.965][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-08 12:46:52.966][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-08 12:46:52.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.969][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-08 12:46:52.969][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-08 12:46:52.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.972][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-08 12:46:52.973][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-08 12:46:52.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.976][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-08 12:46:52.977][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-08 12:46:52.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.980][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-08 12:46:52.981][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-08 12:46:52.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:52.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:52.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:52.984][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-08 12:46:52.984][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-08 12:46:52.999][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-08 12:46:53.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.002][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-08 12:46:53.003][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-08 12:46:53.004][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-08 12:46:53.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.007][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-08 12:46:53.009][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.011][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-08 12:46:53.012][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.013][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:53.014][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.015][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.016][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.017][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.018][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 12:46:53.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:53.020][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.020][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-08 12:46:53.021][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:53.022][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.023][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.024][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:53.024][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:53.024][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:53.024][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 12:46:53.024][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 12:46:53.025][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:53.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:53.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:53.027][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:53.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:53.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:53.029][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.030][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.031][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:53.032][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:53.032][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.033][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.034][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-08 12:46:53.036][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.037][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 12:46:53.038][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.038][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:53.039][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.040][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.041][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.042][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.043][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 12:46:53.043][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:53.044][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.045][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-08 12:46:53.046][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:53.047][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.047][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.048][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:53.048][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:53.048][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:53.048][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-08 12:46:53.048][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-08 12:46:53.049][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:53.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:53.051][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:53.052][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:53.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:53.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:53.054][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.055][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.056][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:53.056][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:53.057][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.058][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.059][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-08 12:46:53.061][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.062][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-08 12:46:53.062][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.063][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:53.064][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.065][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.066][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.067][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.068][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-08 12:46:53.069][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:53.070][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.070][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-08 12:46:53.071][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:53.072][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.073][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.074][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.074][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:53.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:53.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:53.077][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:53.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:53.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:53.080][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.081][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.082][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:53.082][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:53.083][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.084][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.085][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-08 12:46:53.087][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.088][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-08 12:46:53.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:53.090][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.091][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.092][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.093][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.094][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-08 12:46:53.095][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:53.095][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.096][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-08 12:46:53.097][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:53.098][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.099][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.099][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.100][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-08 12:46:53.101][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:53.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:53.103][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:53.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:53.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:53.105][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.106][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.106][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:53.107][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:53.108][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.109][self$setPropertyValue]
biodb.DEBUG[2024-07-08 12:46:53.110][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:53.111][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.119][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.DEBUG[2024-07-08 12:46:53.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.183][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.DEBUG[2024-07-08 12:46:53.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.187][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-08 12:46:53.189][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-08 12:46:53.190][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-08 12:46:53.191][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-08 12:46:53.192][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 12:46:53.194][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-08 12:46:53.195][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-08 12:46:53.196][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-08 12:46:53.197][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-08 12:46:53.198][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-08 12:46:53.199][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 12:46:53.201][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-08 12:46:53.202][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-08 12:46:53.203][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-08 12:46:53.204][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-08 12:46:53.205][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-08 12:46:53.207][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-08 12:46:53.208][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-08 12:46:53.209][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 12:46:53.210][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-08 12:46:53.211][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-08 12:46:53.213][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-08 12:46:53.214][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-08 12:46:53.215][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-08 12:46:53.216][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-08 12:46:53.218][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-08 12:46:53.219][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-08 12:46:53.220][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-08 12:46:53.222][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-08 12:46:53.223][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-08 12:46:53.224][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-08 12:46:53.225][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-08 12:46:53.226][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-08 12:46:53.228][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-08 12:46:53.229][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-08 12:46:53.230][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-08 12:46:53.231][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-08 12:46:53.232][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-08 12:46:53.233][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-08 12:46:53.235][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-08 12:46:53.236][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-08 12:46:53.237][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-08 12:46:53.238][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-08 12:46:53.239][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-08 12:46:53.241][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-08 12:46:53.242][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-08 12:46:53.243][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-08 12:46:53.245][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-08 12:46:53.246][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-08 12:46:53.247][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-08 12:46:53.248][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-08 12:46:53.250][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-08 12:46:53.251][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-08 12:46:53.252][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-08 12:46:53.253][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-08 12:46:53.255][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-08 12:46:53.256][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-08 12:46:53.257][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-08 12:46:53.258][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-08 12:46:53.260][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-08 12:46:53.261][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-08 12:46:53.262][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-08 12:46:53.264][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-08 12:46:53.266][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-08 12:46:53.267][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-08 12:46:53.268][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-08 12:46:53.270][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 12:46:53.271][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 12:46:53.272][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-08 12:46:53.274][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-08 12:46:53.275][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-08 12:46:53.276][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-08 12:46:53.277][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-08 12:46:53.279][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-08 12:46:53.280][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-08 12:46:53.281][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-08 12:46:53.282][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-08 12:46:53.284][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-08 12:46:53.285][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-08 12:46:53.286][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-08 12:46:53.288][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-08 12:46:53.289][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-08 12:46:53.290][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-08 12:46:53.292][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-08 12:46:53.293][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-08 12:46:53.295][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-08 12:46:53.296][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.297][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.308][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.DEBUG[2024-07-08 12:46:53.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-08 12:46:53.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.388][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-08 12:46:53.389][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-08 12:46:53.392][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.393][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.393][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-08 12:46:53.395][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.396][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.397][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.398][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-08 12:46:53.398][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-08 12:46:53.399][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-08 12:46:53.400][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.401][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-08 12:46:53.402][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-08 12:46:53.403][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-08 12:46:53.404][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-08 12:46:53.404][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-08 12:46:53.404][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-08 12:46:53.404][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-08 12:46:53.405][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-08 12:46:53.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:53.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:53.408][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-08 12:46:53.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-08 12:46:53.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-08 12:46:53.410][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-08 12:46:53.411][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:53.411][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-08 12:46:53.412][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-08 12:46:53.412][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-08 12:46:53.413][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-08 12:46:53.414][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-08 12:46:53.414][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-08 12:46:53.415][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-08 12:46:53.417][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-08 12:46:53.418][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-08 12:46:53.419][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-08 12:46:53.421][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-08 12:46:53.422][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-08 12:46:53.426][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-08 12:46:53.427][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-08 12:46:53.428][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-08 12:46:53.429][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-08 12:46:53.430][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-08 12:46:53.431][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-08 12:46:53.440][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-08 12:46:53.442][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-08 12:46:53.443][biodb::testThat]
biodb.INFO [2024-07-08 12:46:53.444][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-07-08 12:46:53.444][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-08 12:46:53.445][biodb::testThat]
biodb.DEBUG[2024-07-08 12:46:53.448][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-08 12:46:53.452][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:53.454][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-08 12:46:53.455][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:53.457][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-08 12:46:53.461][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-08 12:46:53.464][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-08 12:46:53.465][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-07-08 12:46:53.467][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-08 12:46:53.468][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-07-08 12:46:53.473][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-07-08 12:46:53.474][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-08 12:46:53.475][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-07-08 12:46:53.477][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-08 12:46:53.478][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-08 12:46:53.479][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-08 12:46:53.480][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-08 12:46:53.481][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-08 12:46:53.482][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-08 12:46:53.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:53.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:53.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:53.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:53.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:53.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:53.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-08 12:46:53.495][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-07-08 12:46:53.498][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-08 12:46:53.499][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-08 12:46:53.500][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-07-08 12:46:54.138][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-07-08 12:46:54.278][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-08 12:46:54.281][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-07-08 12:46:54.285][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-07-08 12:46:54.288][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-07-08 12:46:54.290][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-08 12:46:54.291][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-08 12:46:54.292][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-08 12:46:54.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-08 12:46:54.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:54.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:54.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:54.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:54.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:54.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-08 12:46:54.309][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:54.310][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:54.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.311][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:54.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:54.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.317][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:54.318][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:54.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.319][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.321][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-08 12:46:54.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-08 12:46:54.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.324][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:54.325][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:54.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.327][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-08 12:46:54.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-08 12:46:54.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.332][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-08 12:46:54.333][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-08 12:46:54.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.334][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.336][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-08 12:46:54.337][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-08 12:46:54.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.338][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.339][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:54.340][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:54.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.342][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.343][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:54.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-08 12:46:54.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.347][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:54.347][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:54.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.349][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.350][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-08 12:46:54.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-08 12:46:54.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.354][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:54.355][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:54.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.356][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:54.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-08 12:46:54.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.361][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:54.362][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:54.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.364][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.365][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-08 12:46:54.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-08 12:46:54.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.369][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:54.369][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:54.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.371][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.372][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-08 12:46:54.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-08 12:46:54.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.376][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:54.377][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:54.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.378][ef$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.380][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-08 12:46:54.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-08 12:46:54.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:54.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:54.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:54.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:54.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:54.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:54.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-08 12:46:54.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-08 12:46:54.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:54.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:54.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:54.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:54.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:54.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:54.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:54.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:54.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:54.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:54.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-08 12:46:54.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-08 12:46:54.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-08 12:46:54.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-08 12:46:54.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-08 12:46:54.415][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-07-08 12:46:54.419][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-08 12:46:54.420][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-08 12:46:54.421][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-08 12:46:54.422][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-08 12:46:54.423][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-08 12:46:54.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-08 12:46:54.424][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-08 12:46:54.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-08 12:46:54.426][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-08 12:46:54.426][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
> 
> proc.time()
   user  system elapsed 
 17.615   1.057  25.643

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.2640.6143.046
ChebiEntry0.2600.0100.279