Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-10-18 20:41 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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 12.7.5 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: 2024-10-17 14:02:51 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 14:04:20 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 88.7 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (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 [2024-10-17 14:03:47.164][biodb::testContext]
biodb.INFO [2024-10-17 14:03:47.169][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:03:47.170][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-17 14:03:47.171][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:03:47.172][biodb::testContext]
biodb.INFO [2024-10-17 14:03:47.181][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:03:47.183][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 14:03:47.194][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:03:47.196][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 14:03:47.197][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 14:03:47.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.201][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 14:03:47.222][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 14:03:47.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.229][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.DEBUG[2024-10-17 14:03:47.231][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 14:03:47.232][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 14:03:47.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.238][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 14:03:47.240][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 14:03:47.241][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 14:03:47.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.263][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 14:03:47.264][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 14:03:47.265][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 14:03:47.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.268][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 14:03:47.269][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 14:03:47.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.272][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 14:03:47.273][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 14:03:47.274][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 14:03:47.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.279][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 14:03:47.279][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 14:03:47.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.283][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 14:03:47.283][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 14:03:47.284][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 14:03:47.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.287][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:03:47.288][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 14:03:47.289][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 14:03:47.290][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 14:03:47.291][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 14:03:47.291][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 14:03:47.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.295][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 14:03:47.296][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 14:03:47.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.300][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 14:03:47.301][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 14:03:47.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.304][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[2024-10-17 14:03:47.305][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 14:03:47.305][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 14:03:47.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.309][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 14:03:47.310][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 14:03:47.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.314][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 14:03:47.315][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 14:03:47.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.318][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:03:47.319][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 14:03:47.342][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 14:03:47.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.349][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[2024-10-17 14:03:47.351][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 14:03:47.352][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 14:03:47.353][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 14:03:47.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.361][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 14:03:47.399][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.421][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-17 14:03:47.422][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:03:47.424][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.425][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.426][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.427][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.428][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:03:47.429][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:03:47.430][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.430][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 14:03:47.431][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:03:47.432][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.433][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.434][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:03:47.434][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:03:47.434][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:03:47.434][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:03:47.434][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:03:47.435][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:03:47.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:03:47.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:03:47.437][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:03:47.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:03:47.441][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:03:47.442][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.443][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.444][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:03:47.445][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:03:47.446][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.447][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.448][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 14:03:47.451][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.453][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:03:47.454][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.456][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:03:47.457][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.458][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.459][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.459][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.460][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:03:47.461][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:03:47.462][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.463][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 14:03:47.464][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:03:47.465][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.466][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.467][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:03:47.467][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:03:47.467][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:03:47.467][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:03:47.467][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:03:47.468][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:03:47.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:03:47.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:03:47.470][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:03:47.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:03:47.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:03:47.473][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.474][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.475][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:03:47.476][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:03:47.476][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.477][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.479][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 14:03:47.482][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.484][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-17 14:03:47.485][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.486][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:03:47.487][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.488][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.489][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.490][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.491][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:03:47.492][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:03:47.500][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.501][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 14:03:47.502][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:03:47.503][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.505][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.507][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.509][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:03:47.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:03:47.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:03:47.515][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:03:47.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:03:47.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:03:47.518][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.519][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.520][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:03:47.520][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:03:47.521][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.522][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.523][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 14:03:47.525][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.526][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:03:47.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.527][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:03:47.528][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.529][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.530][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.531][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:03:47.532][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:03:47.533][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.534][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 14:03:47.535][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:03:47.535][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.536][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.537][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.538][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:03:47.540][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:03:47.541][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:03:47.542][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:03:47.544][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:03:47.545][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:03:47.546][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.548][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.549][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:03:47.550][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:03:47.551][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.552][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:03:47.557][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:03:47.558][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.570][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[2024-10-17 14:03:47.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.574][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[2024-10-17 14:03:47.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.583][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[2024-10-17 14:03:47.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.600][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.DEBUG[2024-10-17 14:03:47.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.603][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[2024-10-17 14:03:47.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.611][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[2024-10-17 14:03:47.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.641][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 14:03:47.648][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 14:03:47.650][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 14:03:47.652][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 14:03:47.655][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:03:47.658][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:03:47.659][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 14:03:47.661][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 14:03:47.663][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 14:03:47.665][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:03:47.668][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:03:47.670][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 14:03:47.672][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 14:03:47.673][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 14:03:47.675][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 14:03:47.676][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:03:47.678][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 14:03:47.680][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 14:03:47.682][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:03:47.683][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 14:03:47.685][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 14:03:47.687][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 14:03:47.688][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 14:03:47.690][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 14:03:47.693][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 14:03:47.695][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 14:03:47.697][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 14:03:47.700][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 14:03:47.701][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 14:03:47.703][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 14:03:47.704][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 14:03:47.705][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 14:03:47.706][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 14:03:47.707][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 14:03:47.709][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 14:03:47.710][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 14:03:47.711][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 14:03:47.712][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 14:03:47.713][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 14:03:47.714][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 14:03:47.716][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 14:03:47.717][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 14:03:47.718][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 14:03:47.719][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 14:03:47.728][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 14:03:47.729][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 14:03:47.730][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 14:03:47.732][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 14:03:47.733][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 14:03:47.734][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 14:03:47.735][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 14:03:47.737][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 14:03:47.738][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 14:03:47.739][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 14:03:47.740][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 14:03:47.741][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 14:03:47.743][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 14:03:47.744][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 14:03:47.745][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 14:03:47.746][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 14:03:47.748][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 14:03:47.750][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 14:03:47.751][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 14:03:47.753][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 14:03:47.754][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 14:03:47.756][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 14:03:47.758][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:03:47.760][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:03:47.761][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 14:03:47.763][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 14:03:47.764][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 14:03:47.765][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 14:03:47.767][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 14:03:47.768][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 14:03:47.769][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 14:03:47.771][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 14:03:47.772][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 14:03:47.773][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 14:03:47.774][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 14:03:47.775][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 14:03:47.777][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 14:03:47.778][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 14:03:47.781][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 14:03:47.790][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 14:03:47.793][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:03:47.798][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:03:47.799][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.801][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:47.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:03:47.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:47.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:47.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:47.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:47.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:47.909][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[2024-10-17 14:03:47.911][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-17 14:03:47.931][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-17 14:03:47.934][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.935][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.936][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.937][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:03:47.937][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.938][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.939][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.940][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-17 14:03:47.941][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 14:03:47.942][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:03:47.943][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.943][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-17 14:03:47.944][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-17 14:03:47.945][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-17 14:03:47.946][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 14:03:47.947][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:03:47.947][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:03:47.947][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:03:47.948][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 14:03:47.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:03:47.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:03:47.950][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:03:47.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:03:47.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:03:47.953][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:03:47.954][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:47.954][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-17 14:03:47.955][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:03:47.956][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:03:47.957][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 14:03:47.958][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-17 14:03:47.958][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-17 14:03:47.965][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:03:47.966][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:03:47.968][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-17 14:03:47.969][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:03:47.971][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:03:47.972][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:03:48.005][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-17 14:03:48.006][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-17 14:03:48.012][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-17 14:03:48.018][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-17 14:03:48.023][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:03:48.025][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:03:48.026][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-17 14:03:48.027][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-17 14:03:48.041][biodb::testThat]
biodb.INFO [2024-10-17 14:03:48.043][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-17 14:03:48.045][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:03:48.046][biodb::testThat]
biodb.TRACE[2024-10-17 14:03:48.052][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[2024-10-17 14:03:48.054][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:48.059][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:48.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:48.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:48.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:48.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:48.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:48.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:48.096][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[2024-10-17 14:03:48.109][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.110][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.112][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.133][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:48.134][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:48.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.136][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.164][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:48.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:48.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.170][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:48.171][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:48.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.174][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.176][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:48.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:48.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.196][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:48.198][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:48.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.200][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.202][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:48.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:48.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.208][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.210][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.212][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.217][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.218][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.219][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.220][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.224][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:48.225][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.226][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.227][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:48.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.234][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.235][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.237][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.244][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:48.245][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:48.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.246][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:48.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:48.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.251][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:48.252][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.254][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.255][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:48.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.258][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:48.259][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:48.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.261][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.262][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:48.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:48.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:48.338][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-10-17 14:03:48.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:48.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:48.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:48.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:48.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.429][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.443][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:03:48.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:03:48.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.450][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:03:48.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:03:48.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.454][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 14:03:48.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 14:03:48.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.457][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 14:03:48.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 14:03:48.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.585][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.586][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.588][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.622][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.623][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.625][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:48.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:48.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:48.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:48.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:48.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:48.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:48.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.650][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:48.651][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:48.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.653][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.654][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:48.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:48.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.667][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:48.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:48.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.672][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:48.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:48.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.675][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:48.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:48.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.679][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:48.681][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:48.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.684][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.685][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:48.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:48.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.717][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.718][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.719][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:48.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.750][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.751][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.752][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:48.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.765][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:48.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:48.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.769][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:48.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:48.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.773][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:48.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:48.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.786][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:48.787][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:48.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.789][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.790][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:48.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:48.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.807][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.812][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.816][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.819][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.820][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.822][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.823][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:48.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.835][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.839][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.842][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.845][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.846][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.848][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.848][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:48.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.860][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:48.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:48.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.864][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:48.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:48.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.867][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:48.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:48.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.871][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:48.872][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:48.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.873][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.874][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:48.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:48.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.900][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.901][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.903][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:48.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:48.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:48.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:48.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:48.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:48.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.933][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:48.934][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:48.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.936][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:48.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:48.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.948][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:48.949][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:48.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.951][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.965][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:48.966][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:48.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.968][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.976][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:48.977][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:48.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.979][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.984][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:48.986][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:48.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.987][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:48.992][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.993][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:48.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:48.995][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.001][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:49.002][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:49.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.004][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.010][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.011][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.013][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.018][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:49.019][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:49.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.021][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.031][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 14:03:49.032][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:49.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.034][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.041][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:49.042][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:49.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.044][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.049][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:49.052][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:49.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.054][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 14:03:49.064][biodb::testThat]
biodb.INFO [2024-10-17 14:03:49.066][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-17 14:03:49.066][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:03:49.067][biodb::testThat]
biodb.DEBUG[2024-10-17 14:03:49.083][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-10-17 14:03:49.093][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:49.099][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-10-17 14:03:49.101][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:03:49.102][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-10-17 14:03:49.104][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:49.133][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:49.135][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:49.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:49.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:49.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:49.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:49.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:49.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:49.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:49.149][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:49.150][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:49.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.153][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:49.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:49.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.185][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:49.187][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:49.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.188][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.190][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:49.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:49.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.195][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:49.196][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:49.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.198][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.200][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:49.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:49.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.204][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:49.204][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:49.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.209][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.211][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:49.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:49.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.215][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.216][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.218][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.223][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:49.224][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:49.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.225][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.226][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:49.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:49.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.230][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:49.231][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.232][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.233][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:49.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.237][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:49.238][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:49.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.239][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:49.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:49.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.245][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:49.246][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:49.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.247][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:49.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:49.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.252][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:49.253][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:49.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.254][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.255][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:49.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:49.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.262][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:49.263][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:49.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.265][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:49.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:49.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:49.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:49.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:49.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:49.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:49.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:49.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:49.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:49.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:49.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:49.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:49.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:49.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:49.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:49.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:49.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:49.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:49.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:49.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:49.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:49.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:49.312][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-10-17 14:03:49.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-17 14:03:49.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-17 14:03:49.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-17 14:03:49.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-17 14:03:49.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-17 14:03:49.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-17 14:03:49.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:03:49.342][biodb::testThat]
biodb.INFO [2024-10-17 14:03:49.343][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-17 14:03:49.345][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:03:49.346][biodb::testThat]
biodb.TRACE[2024-10-17 14:03:49.351][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:49.352][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:49.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.354][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:49.355][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-10-17 14:03:49.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:49.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:49.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:49.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:49.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:49.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:49.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:49.406][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-10-17 14:03:49.412][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-17 14:03:49.436][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:03:49.454][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-17 14:03:49.456][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:03:49.458][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-17 14:03:49.482][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[2024-10-17 14:03:49.486][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:03:49.487][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 14:03:49.488][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:03:49.491][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 14:03:49.501][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-10-17 14:03:49.517][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:49.518][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:49.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.520][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.521][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.522][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.523][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.524][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 14:03:49.530][biodb::testThat]
biodb.INFO [2024-10-17 14:03:49.534][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-17 14:03:49.535][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:03:49.536][biodb::testThat]
biodb.TRACE[2024-10-17 14:03:49.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:49.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:49.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:49.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:49.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:49.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:49.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:49.641][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[2024-10-17 14:03:49.645][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:03:49.646][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 14:03:49.647][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:03:49.649][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-10-17 14:03:49.673][biodb::testThat]
biodb.INFO [2024-10-17 14:03:49.675][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-17 14:03:49.676][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:03:49.677][biodb::testThat]
biodb.TRACE[2024-10-17 14:03:49.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:49.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:49.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.712][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:49.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:49.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.733][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:03:49.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:03:49.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.738][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:03:49.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:03:49.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.742][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 14:03:49.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 14:03:49.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.745][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 14:03:49.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 14:03:49.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:49.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:49.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:49.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:49.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.780][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:49.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:49.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.795][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:03:49.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:03:49.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.801][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 14:03:49.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 14:03:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.806][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 14:03:49.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 14:03:49.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:49.809][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 14:03:49.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 14:03:49.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:49.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:03:49.820][biodb::testThat]
biodb.INFO [2024-10-17 14:03:49.821][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-17 14:03:49.822][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:03:49.824][biodb::testThat]
biodb.INFO [2024-10-17 14:03:49.832][biodb::testThat]
biodb.INFO [2024-10-17 14:03:49.834][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-17 14:03:49.834][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:03:49.836][biodb::testThat]
biodb.INFO [2024-10-17 14:03:49.858][biodb::testThat]
biodb.INFO [2024-10-17 14:03:49.859][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-17 14:03:49.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:03:49.861][biodb::testThat]
biodb.DEBUG[2024-10-17 14:03:49.866][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-10-17 14:03:50.231][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-10-17 14:03:50.519][biodb::testThat]
biodb.INFO [2024-10-17 14:03:50.520][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-17 14:03:50.522][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:03:50.524][biodb::testThat]
biodb.DEBUG[2024-10-17 14:03:50.632][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[2024-10-17 14:03:50.747][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:50.753][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:50.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:50.755][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:50.772][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:50.787][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:50.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:50.789][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 14:03:50.792][biodb::testThat]
biodb.INFO [2024-10-17 14:03:50.793][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-10-17 14:03:50.794][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:03:50.795][biodb::testThat]
biodb.TRACE[2024-10-17 14:03:50.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:50.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:50.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:50.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:50.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:50.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:50.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:50.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:50.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:50.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:50.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:50.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:50.913][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[2024-10-17 14:03:50.917][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:03:50.919][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 14:03:50.920][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:03:50.921][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 14:03:51.002][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[2024-10-17 14:03:51.006][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:03:51.007][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 14:03:51.008][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:03:51.010][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-10-17 14:03:51.026][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:03:51.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:03:51.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:51.071][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[2024-10-17 14:03:51.083][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:03:51.086][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-17 14:03:51.089][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:03:51.091][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-17 14:03:51.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:51.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:51.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:51.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:51.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:51.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:51.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:51.109][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-10-17 14:03:51.161][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:51.163][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-10-17 14:03:51.164][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:51.165][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:51.167][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:51.167][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:51.168][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:51.169][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:51.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:51.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:51.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:51.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:51.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:51.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:51.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:51.183][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-10-17 14:03:51.186][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:51.187][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:51.188][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-10-17 14:03:51.272][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-10-17 14:03:51.340][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:51.343][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-10-17 14:03:51.371][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-10-17 14:03:51.373][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-10-17 14:03:51.374][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:51.375][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:51.376][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:51.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:51.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:51.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:51.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:51.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:51.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:51.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:51.391][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.391][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.392][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.396][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:51.399][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:51.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.401][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.402][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:51.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:51.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.406][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:51.407][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:51.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.409][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.411][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:51.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:51.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.413][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:51.413][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:51.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.414][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:51.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:51.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.416][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:51.416][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:51.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.417][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.419][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:51.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:51.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.424][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:51.425][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:51.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.426][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.428][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:51.429][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.431][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.432][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:51.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.436][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:51.436][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:51.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.438][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:51.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:51.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.443][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:51.444][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:51.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.446][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:51.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:51.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.455][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:51.456][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:51.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.458][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.460][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:51.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:51.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.467][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:51.468][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:51.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.469][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.469][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:51.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:51.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:51.494][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-10-17 14:03:51.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:51.508][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[2024-10-17 14:03:51.510][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:03:51.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-17 14:03:51.511][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:03:51.512][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-17 14:03:51.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:51.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:51.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:51.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:51.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:51.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:51.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:51.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:51.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:51.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:51.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:51.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:51.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:51.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:51.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:51.582][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-10-17 14:03:51.584][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:51.585][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-10-17 14:03:51.587][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:51.588][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:51.589][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:51.590][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:51.591][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:51.592][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:51.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:51.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:51.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:51.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:51.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:51.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:51.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:51.619][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-10-17 14:03:51.636][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:51.638][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:51.655][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-10-17 14:03:51.733][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-10-17 14:03:51.798][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:51.802][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-10-17 14:03:51.812][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-10-17 14:03:51.820][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-10-17 14:03:51.821][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:51.822][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:51.822][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:51.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:51.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:51.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:51.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:51.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:51.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:51.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:51.830][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.833][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.835][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.841][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:51.843][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:51.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.845][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:51.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:51.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.850][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:51.851][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:51.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.853][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:51.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:51.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.861][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:51.862][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:51.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.863][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.865][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:51.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:51.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.868][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:51.869][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:51.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.871][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:51.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:51.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.875][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:51.876][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:51.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.878][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.879][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:51.880][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.882][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.883][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:51.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.886][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:51.887][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:51.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.889][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:51.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:51.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.895][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:51.896][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:51.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.897][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:51.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:51.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.903][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:51.904][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:51.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.906][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.907][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:51.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:51.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.911][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:51.912][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:51.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.913][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.914][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:51.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:51.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:51.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:51.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:51.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:51.955][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-10-17 14:03:51.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:51.970][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[2024-10-17 14:03:51.972][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:03:51.973][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 14:03:51.974][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:03:51.974][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 14:03:51.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:51.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:51.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:51.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:51.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:51.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:51.982][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[2024-10-17 14:03:51.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:51.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:51.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:51.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:51.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:51.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:51.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:51.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:51.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:51.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:51.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:51.993][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-10-17 14:03:51.993][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:51.994][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-10-17 14:03:52.002][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:52.004][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:52.006][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:52.007][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:52.008][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:52.009][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:52.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:52.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:52.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:52.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:52.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:52.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:52.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:52.023][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-10-17 14:03:52.026][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:52.027][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:52.028][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-10-17 14:03:52.105][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-10-17 14:03:52.187][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:52.191][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-10-17 14:03:52.195][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-10-17 14:03:52.199][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-10-17 14:03:52.201][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:52.203][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:52.204][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:52.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:52.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:52.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:52.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:52.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:52.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:52.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:52.221][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.222][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.223][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.226][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:52.227][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:52.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.227][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.231][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:52.236][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:52.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.237][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.237][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:52.238][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:52.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.238][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.239][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:52.239][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:52.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.242][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.243][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:52.243][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:52.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.244][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.244][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:52.246][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.246][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.249][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:52.249][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:52.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.253][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.254][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:52.254][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:52.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.255][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.255][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:52.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:52.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.261][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:52.262][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:52.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.262][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.263][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:52.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:52.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.265][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:52.265][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:52.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.266][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:52.315][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-10-17 14:03:52.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:52.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:52.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:52.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:52.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:52.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:52.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:52.346][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[2024-10-17 14:03:52.347][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-10-17 14:03:52.347][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:52.348][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-10-17 14:03:52.349][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:52.349][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:52.350][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:52.351][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:52.352][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:52.353][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:52.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:52.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:52.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:52.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:52.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:52.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:52.367][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[2024-10-17 14:03:52.368][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-10-17 14:03:52.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:52.372][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:52.374][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-10-17 14:03:52.453][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-10-17 14:03:52.529][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:52.533][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-10-17 14:03:52.537][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-10-17 14:03:52.539][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-10-17 14:03:52.541][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:52.555][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:52.556][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:52.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:52.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:52.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:52.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:52.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:52.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:52.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:52.571][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.573][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.577][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.585][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:52.593][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:52.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.596][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.597][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:52.598][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:52.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.600][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.601][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:52.602][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:52.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.604][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.605][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:52.606][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:52.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.608][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.609][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:52.610][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:52.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.611][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.612][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:52.613][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.615][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.616][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:52.617][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:52.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.619][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.620][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:52.621][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:52.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.623][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:52.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:52.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.628][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:52.629][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:52.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.631][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.632][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:52.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:52.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.635][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:52.636][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:52.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.638][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.649][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:52.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:52.690][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-10-17 14:03:52.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.712][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:52.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:52.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:52.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:52.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:52.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:52.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:52.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:52.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:52.727][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-10-17 14:03:52.728][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:52.731][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-10-17 14:03:52.734][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:52.735][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:52.736][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:52.739][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:52.740][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:52.742][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:52.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:52.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:52.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:52.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:52.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:52.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:52.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:52.756][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-10-17 14:03:52.759][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:52.761][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:52.762][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-10-17 14:03:52.844][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-10-17 14:03:52.921][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:52.926][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-10-17 14:03:52.931][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-10-17 14:03:52.934][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-10-17 14:03:52.938][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:52.941][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:52.943][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:52.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:52.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:52.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:52.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:52.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:52.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:52.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:52.960][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.961][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.963][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:52.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:52.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.967][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:52.968][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:52.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.970][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.971][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:52.972][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:52.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:52.974][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:52.975][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:52.976][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:52.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.023][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.025][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:53.026][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:53.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.028][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.035][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:53.037][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:53.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.038][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.040][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:53.041][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.042][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.043][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:53.044][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:53.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.046][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.047][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:53.048][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:53.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.050][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:53.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:53.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.064][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:53.066][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:53.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.068][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.069][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:53.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:53.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.073][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:53.074][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:53.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.076][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:53.110][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-10-17 14:03:53.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:53.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:53.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:53.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:53.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:53.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:53.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:53.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:53.148][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-10-17 14:03:53.152][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:53.156][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-10-17 14:03:53.157][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:53.158][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:53.159][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:53.160][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:53.161][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:53.162][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:53.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:53.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:53.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:53.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:53.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:53.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:53.180][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[2024-10-17 14:03:53.182][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-10-17 14:03:53.185][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:53.186][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:53.187][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-10-17 14:03:53.280][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-10-17 14:03:53.357][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:53.360][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-10-17 14:03:53.367][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-10-17 14:03:53.370][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-10-17 14:03:53.372][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:53.373][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:53.376][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:53.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:53.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:53.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:53.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:53.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:53.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:53.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:53.395][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.396][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.397][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.402][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:53.403][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:53.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.405][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.409][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:53.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:53.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.414][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:53.415][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:53.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.418][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.421][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:53.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:53.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.426][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:53.427][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:53.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.429][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:53.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:53.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.434][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:53.435][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:53.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.436][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.437][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:53.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:53.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.441][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:53.441][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:53.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.443][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.445][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:53.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:53.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.452][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:53.453][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.454][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.456][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:53.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.470][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:53.472][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:53.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.474][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:53.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:53.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.479][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:53.480][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:53.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.481][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:53.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:53.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.488][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:53.490][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:53.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.494][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.495][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:53.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:53.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.499][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:53.500][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:53.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.502][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.503][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:53.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:53.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:53.555][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-10-17 14:03:53.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:53.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:53.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:53.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:53.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:53.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:53.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:53.581][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[2024-10-17 14:03:53.583][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-10-17 14:03:53.586][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:53.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-10-17 14:03:53.591][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:53.592][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:53.593][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:53.594][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:53.595][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:53.596][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:53.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:53.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:53.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:53.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:53.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:53.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:53.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:53.620][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-10-17 14:03:53.624][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:53.625][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:53.627][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-10-17 14:03:53.703][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-10-17 14:03:53.778][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:53.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-10-17 14:03:53.785][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-10-17 14:03:53.788][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-10-17 14:03:53.790][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:53.791][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:53.794][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:53.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:53.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:53.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:53.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:53.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:53.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:53.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:53.812][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.814][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.815][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.820][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:53.821][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:53.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.822][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.824][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:53.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:53.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.830][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:53.831][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:53.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.833][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:53.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:53.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.838][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:53.839][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:53.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.840][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.841][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:53.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:53.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.844][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:53.845][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:53.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.847][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.848][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:53.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:53.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.852][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:53.852][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:53.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.854][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.855][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:53.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:53.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.859][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:53.861][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.866][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.868][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:53.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.875][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:53.876][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:53.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.878][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:53.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:53.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.883][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:53.884][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:53.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.886][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:53.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:53.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.902][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:53.903][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:53.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.906][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.912][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:53.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:53.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.917][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:53.919][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:53.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.922][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.924][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:53.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:53.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:53.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:53.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:53.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:53.975][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-10-17 14:03:53.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:53.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:53.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:53.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:53.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:53.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:53.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:53.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:53.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:53.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:53.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:53.997][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-10-17 14:03:53.998][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:54.000][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-10-17 14:03:54.001][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:54.002][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:54.003][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:54.004][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:54.005][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:54.005][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:54.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:54.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:54.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:54.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:54.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:54.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:54.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:54.019][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-10-17 14:03:54.022][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:54.039][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:54.041][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-10-17 14:03:54.130][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-10-17 14:03:54.209][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:54.212][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-10-17 14:03:54.216][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-10-17 14:03:54.219][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-10-17 14:03:54.221][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:54.224][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:54.227][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:54.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:54.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:54.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:54.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:54.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:54.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:54.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:54.242][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.244][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.247][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.255][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:54.256][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:54.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.258][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.263][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:54.263][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:54.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.265][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.266][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:54.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:54.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.270][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:54.271][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:54.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.273][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:54.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:54.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.278][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:54.280][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:54.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.283][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:54.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:54.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.289][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:54.289][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:54.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.291][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.292][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:54.293][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.295][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.296][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:54.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.299][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:54.300][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:54.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.302][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:54.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:54.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.308][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:54.311][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:54.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.313][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:54.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:54.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.320][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:54.321][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:54.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.324][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.326][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:54.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:54.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.332][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:54.333][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:54.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.343][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.349][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:54.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:54.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.365][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:54.396][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-10-17 14:03:54.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:54.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:54.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:54.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:54.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:54.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:54.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:54.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:54.419][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-10-17 14:03:54.420][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:54.422][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-10-17 14:03:54.424][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:54.425][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:54.426][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:54.427][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:54.429][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:54.430][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:54.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:54.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:54.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:54.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:54.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:54.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:54.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:54.449][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-10-17 14:03:54.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:54.457][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:54.458][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-10-17 14:03:54.537][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-10-17 14:03:54.610][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:54.613][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-10-17 14:03:54.618][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-10-17 14:03:54.620][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-10-17 14:03:54.622][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:54.624][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:54.625][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:54.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:54.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:54.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:54.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:54.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:54.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:54.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:54.654][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.655][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.657][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.662][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:54.663][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:54.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.664][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.665][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:54.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:54.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.669][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:54.671][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:54.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.673][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.675][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:54.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:54.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.678][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:54.679][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:54.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.681][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:54.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:54.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.689][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:54.690][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:54.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.692][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.693][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:54.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:54.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.697][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:54.700][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:54.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.702][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.704][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:54.705][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.707][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.708][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:54.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.711][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:54.712][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:54.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.714][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:54.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:54.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.718][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:54.719][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:54.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.721][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:54.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:54.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.727][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:54.730][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:54.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.735][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.737][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:54.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:54.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.741][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:54.742][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:54.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.744][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.745][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:54.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:54.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:54.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:54.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:54.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:54.799][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-10-17 14:03:54.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:54.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:54.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:54.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:54.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:54.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:54.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:54.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:54.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:54.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:54.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:54.821][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-10-17 14:03:54.823][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:54.826][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-10-17 14:03:54.828][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:54.829][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:54.830][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:54.831][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:54.832][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:54.833][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:54.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:54.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:54.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:54.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:54.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:54.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:54.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:54.851][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-10-17 14:03:54.854][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:54.856][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:54.858][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-10-17 14:03:54.935][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-10-17 14:03:55.007][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:55.010][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-10-17 14:03:55.015][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-10-17 14:03:55.020][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-10-17 14:03:55.023][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:55.025][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:55.026][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:55.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:55.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:55.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:55.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:55.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:55.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:55.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:55.041][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.042][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.051][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.066][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:55.068][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:55.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.070][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.071][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:55.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:55.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.077][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:55.078][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:55.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.080][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.081][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:55.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:55.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.089][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:55.092][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:55.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.095][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:55.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:55.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.103][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.105][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.107][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.113][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:55.114][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:55.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.115][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.117][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:55.118][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.119][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.122][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:55.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.127][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.128][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.129][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.134][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:55.135][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:55.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.137][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:55.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:55.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.141][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:55.142][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:55.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.144][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.145][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:55.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:55.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.149][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:55.150][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:55.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.154][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.158][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:55.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:55.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:55.214][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-10-17 14:03:55.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:55.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:55.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:55.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:55.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:55.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:55.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:55.241][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[2024-10-17 14:03:55.242][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-10-17 14:03:55.243][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:55.246][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-10-17 14:03:55.249][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:55.250][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:55.252][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:55.253][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:55.254][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:55.255][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:55.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:55.259][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:55.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:55.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:55.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:55.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:55.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:55.274][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-10-17 14:03:55.278][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:55.279][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:55.281][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-10-17 14:03:55.364][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-10-17 14:03:55.437][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:55.441][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-10-17 14:03:55.446][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-10-17 14:03:55.449][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-10-17 14:03:55.450][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:55.451][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:55.452][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:55.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:55.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:55.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:55.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:55.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:55.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:55.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:55.466][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.467][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.469][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.475][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:55.478][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:55.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.480][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.481][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:55.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:55.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.484][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:55.485][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:55.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.498][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:55.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:55.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.503][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:55.504][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:55.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.505][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:55.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:55.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.510][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.510][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.512][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.513][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.517][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:55.518][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:55.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.519][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.520][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:55.522][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.523][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.524][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:55.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.528][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.529][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.530][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.538][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:55.539][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:55.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.541][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:55.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:55.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.546][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:55.547][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:55.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.549][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.551][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:55.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:55.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.555][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:55.556][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:55.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.558][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.559][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:55.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:55.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:55.607][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-10-17 14:03:55.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:55.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:55.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:55.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:55.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:55.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:55.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:55.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:55.636][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-10-17 14:03:55.637][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:55.640][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-10-17 14:03:55.641][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:55.642][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:55.644][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:55.645][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:55.646][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:55.647][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:55.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:55.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:55.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:55.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:55.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:55.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:55.660][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[2024-10-17 14:03:55.661][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-10-17 14:03:55.664][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:55.665][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:55.666][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-10-17 14:03:55.745][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-10-17 14:03:55.821][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:55.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-10-17 14:03:55.828][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-10-17 14:03:55.831][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-10-17 14:03:55.832][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:55.833][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:55.835][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:55.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:55.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:55.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:55.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:55.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:55.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:55.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:55.852][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.853][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.855][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.859][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:55.860][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:55.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.862][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.863][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:55.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:55.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.869][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:55.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:55.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.873][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.879][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:55.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:55.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.889][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:55.892][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:55.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.894][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:55.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:55.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.921][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.922][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.924][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:55.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.931][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:55.932][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:55.933][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.934][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.935][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:55.936][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.937][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.937][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.939][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:55.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:55.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.942][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.943][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.945][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:55.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.952][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:55.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:55.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.955][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:55.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:55.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.962][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:55.963][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:55.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.964][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.966][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:55.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:55.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.969][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:55.970][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:55.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.972][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.973][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:55.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:55.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:55.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:55.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:55.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:55.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:55.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:56.017][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-10-17 14:03:56.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:56.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:56.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:56.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:56.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:56.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:56.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:56.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:56.050][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-10-17 14:03:56.051][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:56.053][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-10-17 14:03:56.056][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:56.058][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:56.059][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:56.060][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:56.061][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:56.062][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:56.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:56.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:56.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:56.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:56.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:56.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:56.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:56.076][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-10-17 14:03:56.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:56.081][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:56.083][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-10-17 14:03:56.158][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-10-17 14:03:56.235][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:56.238][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-10-17 14:03:56.242][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-10-17 14:03:56.244][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-10-17 14:03:56.246][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:56.247][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:56.248][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:56.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:56.251][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:56.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:56.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:56.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:56.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:56.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:56.265][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.266][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.268][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.273][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:56.274][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:56.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.275][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.276][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:56.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:56.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.281][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:56.283][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:56.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.286][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.287][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:56.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:56.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.291][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:56.291][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:56.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.293][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.294][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:56.295][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:56.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.297][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.298][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:56.299][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:56.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.301][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.304][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:56.306][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.308][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.309][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:56.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.323][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:56.325][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:56.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.327][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:56.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:56.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.333][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:56.334][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:56.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.336][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:56.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:56.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.342][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:56.344][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:56.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.346][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.348][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:56.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:56.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.351][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:56.352][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:56.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.354][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:56.408][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-10-17 14:03:56.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:56.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:56.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:56.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:56.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:56.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:56.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:56.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:56.443][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-10-17 14:03:56.444][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:56.445][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-10-17 14:03:56.446][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:56.447][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:56.448][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:56.449][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:56.450][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:56.451][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:56.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:56.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:56.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:56.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:56.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:56.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:56.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:56.476][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-10-17 14:03:56.479][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:56.480][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:56.482][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-10-17 14:03:56.557][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-10-17 14:03:56.639][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:56.642][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-10-17 14:03:56.646][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-10-17 14:03:56.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-10-17 14:03:56.650][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:56.651][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:56.652][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:56.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:56.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:56.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:56.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:56.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:56.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:56.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:56.669][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.670][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.672][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.677][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:56.678][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:56.679][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.680][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.682][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:56.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:56.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.686][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:56.687][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:56.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.691][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:56.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:56.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.697][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:56.698][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:56.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.700][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.702][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:56.703][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:56.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.704][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.705][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:56.706][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:56.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.708][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.709][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:56.710][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.711][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.713][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:56.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.719][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:56.721][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:56.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.723][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:56.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:56.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.729][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:56.730][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:56.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.732][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.733][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:56.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:56.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.738][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:56.739][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:56.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.740][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.741][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:56.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:56.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.752][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:56.757][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:56.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.759][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:56.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:56.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:56.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:56.801][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-10-17 14:03:56.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:56.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:56.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:56.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:56.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:56.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:56.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:56.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:56.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:56.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:56.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:56.824][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-10-17 14:03:56.825][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:56.826][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-10-17 14:03:56.828][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:56.829][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:56.830][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:56.831][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:56.832][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:56.834][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:56.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:56.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:56.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:56.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:56.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:56.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:56.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:56.849][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-10-17 14:03:56.852][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:56.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:56.855][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-10-17 14:03:56.931][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-10-17 14:03:57.004][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:57.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-10-17 14:03:57.007][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-10-17 14:03:57.009][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-10-17 14:03:57.010][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:57.010][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:57.021][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:57.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:57.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:57.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:57.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:57.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:57.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:57.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:57.034][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.035][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.035][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.038][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:57.040][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:57.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.042][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.043][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:57.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:57.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.050][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:57.051][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:57.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.053][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:57.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:57.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.058][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:57.059][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:57.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.061][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:57.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:57.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.065][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.066][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.069][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.076][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:57.077][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:57.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.078][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.080][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:57.081][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.083][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.084][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:57.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.088][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.089][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.090][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.096][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:57.097][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:57.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.100][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:57.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:57.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.103][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:57.103][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:57.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.106][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.107][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:57.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:57.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.109][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:57.109][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:57.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.110][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.110][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:57.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:57.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:57.159][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-10-17 14:03:57.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:57.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:57.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:57.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:57.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:57.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:57.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:57.185][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[2024-10-17 14:03:57.185][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-10-17 14:03:57.186][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:57.187][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-10-17 14:03:57.187][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:57.187][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:57.188][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:57.188][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:57.189][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:57.189][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:57.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:57.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:57.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:57.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:57.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:57.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:57.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:57.205][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-10-17 14:03:57.206][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:57.207][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:57.208][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-10-17 14:03:57.286][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-10-17 14:03:57.354][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:57.355][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-10-17 14:03:57.361][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-10-17 14:03:57.365][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-10-17 14:03:57.367][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:57.368][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:57.369][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:57.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:57.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:57.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:57.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:57.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:57.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:57.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:57.395][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.396][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.398][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.403][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:57.403][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:57.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.404][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.404][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:57.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:57.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.406][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:57.406][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:57.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.407][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.407][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:57.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:57.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.409][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:57.411][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:57.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.413][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:57.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:57.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.418][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.419][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.421][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.426][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:57.427][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:57.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.428][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.430][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:57.431][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.432][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.434][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:57.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.439][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.439][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.440][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.442][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:57.442][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:57.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.443][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:57.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:57.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.445][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:57.445][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:57.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.446][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.447][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:57.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:57.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.451][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:57.452][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:57.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.454][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.455][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:57.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:57.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:57.510][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-10-17 14:03:57.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:57.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:57.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:57.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:57.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:57.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:57.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:57.521][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[2024-10-17 14:03:57.522][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-10-17 14:03:57.522][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:57.524][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-10-17 14:03:57.525][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:57.525][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:57.526][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:57.526][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:57.527][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:57.527][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:57.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:57.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:57.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:57.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:57.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:57.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:57.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:57.542][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-10-17 14:03:57.545][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:57.547][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:57.548][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-10-17 14:03:57.616][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-10-17 14:03:57.677][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:57.678][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-10-17 14:03:57.681][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-10-17 14:03:57.684][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-10-17 14:03:57.687][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:57.689][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:57.690][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:57.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:57.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:57.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:57.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:57.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:57.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:57.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:57.705][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.706][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.707][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.712][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:57.713][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:57.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.727][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.733][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:57.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:57.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.736][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:57.737][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:57.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.738][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.739][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:57.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:57.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.747][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:57.747][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:57.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.748][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:57.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:57.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.756][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.757][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.758][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:57.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.760][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:57.761][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:57.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.762][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.763][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:57.764][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.766][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.767][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:57.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.773][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.774][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.776][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:57.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.781][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:57.782][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:57.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.783][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:57.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:57.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.788][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:57.789][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:57.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.792][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.793][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:57.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:57.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.799][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:57.800][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:57.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.802][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.803][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:57.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:57.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:57.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:57.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:57.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:57.846][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-10-17 14:03:57.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:57.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:57.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:57.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:57.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:57.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:57.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:57.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:57.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:57.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:57.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:57.869][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-10-17 14:03:57.870][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:57.872][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-10-17 14:03:57.873][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:57.875][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:57.876][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:57.876][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:57.877][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:57.877][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:57.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:57.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:57.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:57.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:57.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:57.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:57.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:57.894][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-10-17 14:03:57.899][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:57.903][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:57.905][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-10-17 14:03:57.980][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-10-17 14:03:58.044][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:58.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-10-17 14:03:58.050][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-10-17 14:03:58.053][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-10-17 14:03:58.055][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:58.056][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:58.057][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:58.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:58.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:58.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:58.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:58.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:58.066][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:58.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:58.069][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.070][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.073][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.080][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:58.081][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:58.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.082][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.083][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:58.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:58.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.086][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:58.087][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:58.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.088][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.089][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:58.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:58.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.099][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:58.109][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:58.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.117][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:58.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:58.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.123][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.124][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.126][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.127][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.132][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:58.133][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:58.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.136][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.137][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:58.138][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.140][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.142][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:58.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.145][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.146][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.148][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.153][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:58.154][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:58.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.155][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:58.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:58.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.160][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:58.161][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:58.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.162][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.165][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:58.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:58.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:58.173][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:58.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.175][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.177][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:58.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:58.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:58.219][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-10-17 14:03:58.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:58.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:58.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:58.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:58.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:58.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:58.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:58.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:58.258][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-10-17 14:03:58.259][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:58.260][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-10-17 14:03:58.261][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:58.262][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:58.264][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:58.265][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:58.266][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:58.266][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:58.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:58.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:58.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:58.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:58.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:58.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:58.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:58.284][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-10-17 14:03:58.287][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:58.288][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:58.289][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-10-17 14:03:58.372][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-10-17 14:03:58.443][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:58.447][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-10-17 14:03:58.451][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-10-17 14:03:58.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-10-17 14:03:58.457][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:58.458][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:58.460][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:58.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:58.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:58.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:58.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:58.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:58.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:58.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:58.479][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.480][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.482][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.486][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:58.487][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:58.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.489][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.490][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:58.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:58.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.494][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:58.495][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:58.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.498][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.500][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:58.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:58.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.504][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:58.505][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:58.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.509][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:58.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:58.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.515][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.516][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.518][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.539][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:58.541][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:58.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.543][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.545][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:58.546][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.548][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.549][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:58.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.553][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.554][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.556][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.564][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:58.565][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:58.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.567][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:58.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:58.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.572][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:58.573][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:58.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.575][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.576][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:58.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:58.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.581][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:58.582][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:58.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.583][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.585][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:58.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:58.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:58.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:58.629][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-10-17 14:03:58.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:58.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:58.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:58.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:58.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:58.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:58.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:58.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:58.664][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-10-17 14:03:58.667][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:58.669][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-10-17 14:03:58.671][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:58.672][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:58.673][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:58.674][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:58.675][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:58.676][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:58.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:58.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:58.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:58.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:58.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:58.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:58.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:58.692][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-10-17 14:03:58.696][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:58.697][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:58.699][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-10-17 14:03:58.781][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-10-17 14:03:58.860][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:58.863][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-10-17 14:03:58.867][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-10-17 14:03:58.871][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-10-17 14:03:58.875][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:58.877][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:58.879][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:58.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:58.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:58.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:58.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:58.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:58.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:58.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:58.896][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.898][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.900][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:58.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:58.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.905][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:58.906][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:58.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.907][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.909][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:58.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:58.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.913][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:58.914][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:58.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.916][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.918][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:58.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:58.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.922][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:58.923][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:58.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.926][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:58.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:58.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.934][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.935][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.937][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.939][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:58.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.945][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:58.946][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:58.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.948][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.949][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:58.950][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.952][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.953][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:58.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:58.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.968][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.969][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.972][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:58.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.978][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:58.978][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:58.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.980][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.982][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:58.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:58.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.986][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:58.987][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:58.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.988][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.990][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:58.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:58.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.995][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:58.996][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:58.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:58.998][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:58.999][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:59.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:59.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.051][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-10-17 14:03:59.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:59.082][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-10-17 14:03:59.083][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:03:59.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-10-17 14:03:59.086][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:03:59.088][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:03:59.089][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:03:59.090][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:03:59.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:03:59.092][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:03:59.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:03:59.118][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-10-17 14:03:59.120][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:03:59.122][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:03:59.123][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-10-17 14:03:59.202][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-10-17 14:03:59.272][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:03:59.275][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-10-17 14:03:59.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-10-17 14:03:59.287][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-10-17 14:03:59.289][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:03:59.290][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:03:59.291][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:03:59.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.308][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.309][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.311][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.316][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:59.317][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:59.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.318][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.319][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:03:59.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:03:59.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.326][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:59.327][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:59.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.329][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.330][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:03:59.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:03:59.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.334][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:59.334][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:59.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.336][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:03:59.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:03:59.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.341][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:59.342][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:59.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.343][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:03:59.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:03:59.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.349][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:59.351][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:03:59.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.353][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.355][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:59.356][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.358][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.359][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:03:59.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.363][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:59.363][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:59.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.365][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:59.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:03:59.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.370][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:59.371][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:59.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.385][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:03:59.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:03:59.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.393][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:59.394][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:59.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.397][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.399][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:03:59.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:03:59.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.403][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:59.404][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:59.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.406][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.408][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:03:59.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:03:59.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:03:59.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:03:59.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:03:59.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.451][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-10-17 14:03:59.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.489][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[2024-10-17 14:03:59.493][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:03:59.495][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 14:03:59.496][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:03:59.498][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 14:03:59.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.552][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[2024-10-17 14:03:59.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.628][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.TRACE[2024-10-17 14:03:59.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.702][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.TRACE[2024-10-17 14:03:59.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.843][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.949][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[2024-10-17 14:03:59.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:03:59.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:03:59.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:03:59.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:03:59.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:03:59.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:03:59.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:03:59.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:03:59.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:03:59.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:03:59.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:03:59.998][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.TRACE[2024-10-17 14:03:59.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:00.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:00.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:00.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:00.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:00.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:00.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:00.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:00.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:00.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:00.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:00.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:00.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:00.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:00.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:00.056][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.TRACE[2024-10-17 14:04:00.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:00.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:00.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:00.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:00.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:00.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:00.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:00.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:00.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:00.153][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[2024-10-17 14:04:00.166][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:04:00.167][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:04:00.170][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-17 14:04:00.242][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-17 14:04:00.315][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:04:00.320][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-10-17 14:04:00.325][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-10-17 14:04:00.329][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:00.333][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:04:00.334][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:04:00.336][private$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[2024-10-17 14:04:00.408][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[2024-10-17 14:04:00.484][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:04:00.487][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-10-17 14:04:00.492][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-10-17 14:04:00.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:00.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:00.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:00.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:00.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:00.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:00.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:00.507][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-10-17 14:04:00.508][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:04:00.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-10-17 14:04:00.513][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:04:00.515][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:04:00.516][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:04:00.517][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:04:00.518][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:04:00.519][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:04:00.522][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:00.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:00.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:00.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:00.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:00.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:00.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:00.537][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-10-17 14:04:00.540][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:04:00.541][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 14:04:00.542][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-10-17 14:04:00.615][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-10-17 14:04:00.689][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:04:00.692][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-10-17 14:04:00.696][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-10-17 14:04:00.699][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-10-17 14:04:00.700][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:04:00.702][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:04:00.703][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:04:00.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:00.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:00.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:00.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:00.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:00.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:00.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:00.722][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:00.723][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:00.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.725][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:00.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:00.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.730][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:00.738][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:00.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.752][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.754][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:00.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:00.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.758][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:00.759][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:00.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.761][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.762][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:00.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:00.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.766][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:00.767][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:00.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.768][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.769][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:00.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:00.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.774][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:00.776][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:00.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.777][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:00.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:00.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.784][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:00.785][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:00.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.787][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.788][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:00.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:00.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.791][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:00.792][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.795][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.797][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:00.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:00.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.802][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.803][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.805][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.809][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:00.810][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:00.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.812][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:00.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:00.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.820][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:00.821][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:00.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.823][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.824][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:00.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:00.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.828][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:00.829][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:00.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.830][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.832][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:00.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:00.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:00.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:00.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:00.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:00.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:00.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:00.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:00.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:00.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:00.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:00.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:00.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:00.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:00.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:00.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:00.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:00.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:00.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:00.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:00.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:00.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:00.885][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-10-17 14:04:00.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:00.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:00.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:00.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:00.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:00.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:00.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:00.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:00.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:00.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:00.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:00.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:00.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:00.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:00.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:00.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:00.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:00.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:00.937][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[2024-10-17 14:04:00.938][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-10-17 14:04:00.939][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:04:00.940][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-10-17 14:04:00.942][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 14:04:00.943][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 14:04:00.944][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:04:00.945][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:04:00.946][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 14:04:00.947][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 14:04:00.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:00.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:00.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:00.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:00.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:00.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:00.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:00.961][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-10-17 14:04:00.964][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 14:04:00.965][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-10-17 14:04:00.966][rule$waitAsNeeded] Wait 0.202639 second(s).
biodb.TRACE[2024-10-17 14:04:01.321][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-10-17 14:04:01.399][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-10-17 14:04:01.473][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 14:04:01.476][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-10-17 14:04:01.482][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-10-17 14:04:01.485][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-10-17 14:04:01.487][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 14:04:01.488][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:04:01.489][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:04:01.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:01.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:01.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:01.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:01.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:01.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:01.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:01.523][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:01.524][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:01.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.525][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:01.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:01.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.533][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:01.534][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:01.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.537][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.539][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:01.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:01.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.544][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:01.545][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:01.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.547][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:01.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:01.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.553][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:01.554][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:01.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.555][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:01.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:01.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.562][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:01.563][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:01.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.565][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:01.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:01.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.570][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:01.571][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:01.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.573][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.574][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:01.577][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:01.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.580][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.582][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:01.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:01.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.586][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.587][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.588][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.593][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:01.594][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:01.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.595][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.597][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:01.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:01.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.600][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:01.601][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:01.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.604][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.605][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:01.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:01.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.609][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:01.610][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:01.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.612][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.613][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:01.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:01.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:01.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:01.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:01.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:01.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:01.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:01.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:01.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:01.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:01.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:01.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:01.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:01.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:01.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:01.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:01.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:01.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:01.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:01.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:01.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:01.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:01.666][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-10-17 14:04:01.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:01.706][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:01.709][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:01.711][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 14:04:01.713][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:01.716][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 14:04:01.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:01.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:01.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:01.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:01.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:01.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:01.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:01.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:01.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:01.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:01.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:01.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:01.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:01.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:01.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:01.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:01.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:01.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:01.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:01.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:01.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:01.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:01.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:01.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:01.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:01.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:01.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:01.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:01.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:01.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:01.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:01.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:01.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:01.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:01.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:01.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:01.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:01.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:01.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:01.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:01.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:01.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:01.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:01.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:01.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:01.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:01.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:01.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:01.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:01.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.306][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.563][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:02.567][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:02.569][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 14:04:02.571][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:02.583][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 14:04:02.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.611][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.644][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.849][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.862][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:02.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:02.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:02.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:02.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:02.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:02.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:02.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:02.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:02.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:02.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:02.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.086][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.164][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 14:04:03.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 14:04:03.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:03.184][biodb::testThat]
biodb.INFO [2024-10-17 14:04:03.187][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-10-17 14:04:03.189][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:03.192][biodb::testThat]
biodb.TRACE[2024-10-17 14:04:03.196][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:03.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:03.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:03.235][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:03.240][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:03.242][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-17 14:04:03.243][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:03.245][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-17 14:04:03.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.272][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:03.277][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:03.279][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-17 14:04:03.280][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:03.281][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-17 14:04:03.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:03.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.347][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 14:04:03.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.368][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.369][private$selectFields]
biodb.TRACE[2024-10-17 14:04:03.370][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:03.370][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:03.371][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.372][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.373][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.376][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.379][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.382][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.385][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.386][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.387][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.392][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.394][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:03.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.421][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-17 14:04:03.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.453][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.454][private$selectFields]
biodb.TRACE[2024-10-17 14:04:03.455][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:03.456][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:03.457][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.458][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.459][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.460][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.461][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.462][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.464][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.465][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.466][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.466][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.470][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.472][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.474][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:03.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.488][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 14:04:03.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.513][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.514][private$selectFields]
biodb.TRACE[2024-10-17 14:04:03.514][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:03.515][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:03.516][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.517][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.518][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.519][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.520][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.521][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.523][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.523][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.524][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.525][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.526][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.527][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.528][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:03.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.539][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-17 14:04:03.540][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 14:04:03.541][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 14:04:03.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:03.644][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:03.650][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:03.651][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-17 14:04:03.653][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:03.654][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-17 14:04:03.660][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:03.663][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:03.665][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-17 14:04:03.666][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:03.668][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-17 14:04:03.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:03.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:03.780][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 14:04:03.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.835][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.836][private$selectFields]
biodb.TRACE[2024-10-17 14:04:03.838][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:03.839][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:03.840][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.841][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.842][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.843][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.844][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.845][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.846][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.848][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.849][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.850][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.852][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.854][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.855][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:03.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.870][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-17 14:04:03.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.927][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.928][private$selectFields]
biodb.TRACE[2024-10-17 14:04:03.929][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:03.930][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:03.931][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.932][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.933][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.937][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.938][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.939][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.941][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.941][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.952][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.954][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.956][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.958][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.959][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:03.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.972][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 14:04:03.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:03.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:03.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:03.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:03.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:03.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:03.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:03.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:03.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:03.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:03.998][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:03.999][private$selectFields]
biodb.TRACE[2024-10-17 14:04:04.000][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:04.001][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:04.002][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.002][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.003][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.005][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.006][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.007][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.008][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.009][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.010][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.010][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.011][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.013][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.014][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:04.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.029][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-17 14:04:04.029][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 14:04:04.030][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 14:04:04.040][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 14:04:04.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 14:04:04.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:04.049][biodb::testThat]
biodb.INFO [2024-10-17 14:04:04.050][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-10-17 14:04:04.051][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:04.052][biodb::testThat]
biodb.TRACE[2024-10-17 14:04:04.056][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:04.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:04.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:04.098][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:04.102][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:04.103][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-17 14:04:04.104][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:04.106][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-17 14:04:04.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.131][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:04.135][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:04.137][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-17 14:04:04.138][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:04.139][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-17 14:04:04.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.200][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 14:04:04.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.222][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.223][private$selectFields]
biodb.TRACE[2024-10-17 14:04:04.224][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:04.224][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:04.225][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.226][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.227][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.228][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.231][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.234][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.235][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.236][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.237][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.239][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.241][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:04.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.252][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-17 14:04:04.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.273][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.274][private$selectFields]
biodb.TRACE[2024-10-17 14:04:04.274][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:04.276][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:04.278][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.280][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.281][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.283][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.284][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.284][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.286][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.287][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.288][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.288][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.289][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.291][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.292][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:04.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.308][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 14:04:04.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.328][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.329][private$selectFields]
biodb.TRACE[2024-10-17 14:04:04.330][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:04.331][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:04.331][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.332][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.333][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.335][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.336][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.336][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.338][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.339][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.340][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.340][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.343][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.344][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:04.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.355][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-17 14:04:04.356][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 14:04:04.357][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 14:04:04.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.399][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:04.404][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:04.408][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:04.409][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-17 14:04:04.411][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:04.412][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-17 14:04:04.416][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:04.422][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:04.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-17 14:04:04.426][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:04.428][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-17 14:04:04.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:04.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.504][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 14:04:04.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.526][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.527][private$selectFields]
biodb.TRACE[2024-10-17 14:04:04.528][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:04.529][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:04.529][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.530][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.531][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.533][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.533][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.534][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.536][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.537][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.538][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.538][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.539][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.541][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.542][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:04.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.564][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-17 14:04:04.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.584][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.585][private$selectFields]
biodb.TRACE[2024-10-17 14:04:04.586][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:04.587][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:04.587][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.588][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.589][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.591][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.591][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.592][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.594][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.595][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.595][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.596][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.597][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.599][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.599][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:04.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.614][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 14:04:04.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.637][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.637][private$selectFields]
biodb.TRACE[2024-10-17 14:04:04.638][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:04.639][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:04.640][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.641][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.642][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.643][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.644][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.645][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.647][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.648][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.649][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.649][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.651][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.654][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.655][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:04.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.671][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-17 14:04:04.672][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 14:04:04.673][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 14:04:04.682][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 14:04:04.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 14:04:04.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:04.693][biodb::testThat]
biodb.INFO [2024-10-17 14:04:04.694][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-10-17 14:04:04.695][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:04.696][biodb::testThat]
biodb.TRACE[2024-10-17 14:04:04.699][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 14:04:04.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 14:04:04.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:04.745][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:04.749][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:04.752][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-17 14:04:04.754][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:04.755][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-17 14:04:04.758][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.787][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:04.790][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:04.792][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-17 14:04:04.793][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:04.794][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-17 14:04:04.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:04.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:04.851][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 14:04:04.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:04.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.873][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.874][private$selectFields]
biodb.TRACE[2024-10-17 14:04:04.877][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:04.878][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:04.879][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.881][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.882][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.883][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.884][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.885][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.887][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.888][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.888][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.889][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.890][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.892][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.892][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:04.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.909][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-17 14:04:04.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:04.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:04.929][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[2024-10-17 14:04:04.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.937][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.938][private$selectFields]
biodb.TRACE[2024-10-17 14:04:04.939][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:04.939][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:04.940][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.941][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.942][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.943][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.944][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.945][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.947][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.947][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.948][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:04.949][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.953][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.954][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.955][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:04.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:04.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:04.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:04.990][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 14:04:04.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:04.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:04.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:04.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:04.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.008][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.009][private$selectFields]
biodb.TRACE[2024-10-17 14:04:05.010][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:05.010][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:05.011][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.014][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.017][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.018][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.019][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.024][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.026][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.027][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.028][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.029][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.030][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.031][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:05.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.042][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-17 14:04:05.043][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 14:04:05.046][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 14:04:05.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:05.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:05.118][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:05.122][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:05.123][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-17 14:04:05.125][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:05.126][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-17 14:04:05.129][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:05.133][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:05.134][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-17 14:04:05.135][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:05.137][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-17 14:04:05.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:05.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:05.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:05.217][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 14:04:05.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.244][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.244][private$selectFields]
biodb.TRACE[2024-10-17 14:04:05.245][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:05.246][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:05.247][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.247][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.248][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.250][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.251][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.252][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.253][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.254][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.255][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.256][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.256][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.258][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.259][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:05.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.273][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-17 14:04:05.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.294][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.295][private$selectFields]
biodb.TRACE[2024-10-17 14:04:05.296][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:05.297][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:05.297][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.298][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.299][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.301][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.302][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.302][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.305][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.310][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.312][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.313][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.314][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.316][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.317][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:05.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.328][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 14:04:05.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.349][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.349][private$selectFields]
biodb.TRACE[2024-10-17 14:04:05.350][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 14:04:05.351][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 14:04:05.352][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.353][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.353][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.355][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.357][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.360][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.362][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.363][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.364][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 14:04:05.365][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.367][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.375][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.377][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 14:04:05.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.389][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-17 14:04:05.390][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 14:04:05.393][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 14:04:05.419][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 14:04:05.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 14:04:05.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:05.429][biodb::testThat]
biodb.INFO [2024-10-17 14:04:05.430][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-10-17 14:04:05.431][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:05.432][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:05.434][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-10-17 14:04:05.435][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:04:05.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-10-17 14:04:05.438][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:05.440][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml".
biodb.DEBUG[2024-10-17 14:04:05.441][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:04:05.443][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:04:05.444][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:04:05.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.458][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.459][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.461][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.465][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:05.466][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:05.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.468][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.469][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:05.470][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:05.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.471][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.473][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:05.474][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:05.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.475][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.476][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.477][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.478][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.480][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.480][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.482][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.483][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:05.484][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:05.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.486][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.487][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.489][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.493][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.494][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:05.495][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:05.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.498][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.500][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:05.502][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:05.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.504][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.505][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:05.506][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:05.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.508][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:05.553][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-10-17 14:04:05.554][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-17 14:04:05.563][biodb::testThat]
biodb.INFO [2024-10-17 14:04:05.564][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-10-17 14:04:05.565][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:05.565][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:05.576][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-10-17 14:04:05.578][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-10-17 14:04:05.579][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-10-17 14:04:05.581][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-10-17 14:04:05.582][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-10-17 14:04:05.585][loadFileContents] Loaded 3 files from cache: [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2024-10-17 14:04:05.586][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:04:05.587][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-10-17 14:04:05.588][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-10-17 14:04:05.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.607][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.610][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.614][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:05.615][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:05.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.617][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.618][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:05.619][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:05.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.621][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.622][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:05.623][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:05.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.624][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.625][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.627][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.630][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.632][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.633][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.634][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.636][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:05.638][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:05.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.640][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.642][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.643][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.645][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.646][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:05.647][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:05.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.649][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.650][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:05.651][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:05.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.653][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.654][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:05.655][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:05.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.657][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:05.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.706][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.707][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.709][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.718][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:05.720][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:05.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.722][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.723][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:05.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:05.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.727][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:05.728][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:05.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.730][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.731][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:05.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:05.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.736][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:05.737][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:05.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.739][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:05.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:05.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.744][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.745][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.746][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.751][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.752][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.753][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.754][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.758][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:05.759][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:05.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.768][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.769][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:05.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:05.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.772][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.773][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.775][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.779][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:05.780][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:05.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.781][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:05.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:05.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.791][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:05.792][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:05.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.796][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.798][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:05.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:05.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.802][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:05.803][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:05.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.805][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.807][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:05.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:05.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:05.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:05.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:05.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:05.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:05.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:05.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:05.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:05.855][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.857][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.860][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.866][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:05.867][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:05.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.868][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.870][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:05.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:05.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.873][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:05.874][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:05.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.876][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.877][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:05.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:05.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.880][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:05.881][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:05.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.882][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:05.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:05.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.887][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.888][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.889][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.891][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:05.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.894][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.895][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.896][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.898][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:05.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.901][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:05.902][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:05.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.904][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.905][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:05.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:05.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.908][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.909][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.911][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:05.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.915][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:05.916][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:05.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.917][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:05.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:05.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.927][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:05.928][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:05.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.929][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.930][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:05.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:05.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.938][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:05.939][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:05.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.941][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.942][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:05.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:05.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:05.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:05.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:05.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:05.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:05.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:06.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:06.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:06.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:06.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:06.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:06.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:06.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:06.006][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-10-17 14:04:06.007][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-10-17 14:04:06.008][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-10-17 14:04:06.024][biodb::testThat]
biodb.INFO [2024-10-17 14:04:06.026][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-10-17 14:04:06.026][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:06.027][biodb::testThat]
biodb.INFO [2024-10-17 14:04:06.054][biodb::testThat]
biodb.INFO [2024-10-17 14:04:06.056][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-10-17 14:04:06.057][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:06.057][biodb::testThat]
biodb.INFO [2024-10-17 14:04:06.069][biodb::testThat]
biodb.INFO [2024-10-17 14:04:06.070][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-10-17 14:04:06.071][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:06.072][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:06.074][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:06.078][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:06.079][cch$loadFileContent] Trying to load 1 files from cache: [1]: "aed2cd6d5d221333c0a30a9f8dbc41b4".
biodb.TRACE[2024-10-17 14:04:06.081][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:06.086][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content".
biodb.TRACE[2024-10-17 14:04:06.099][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:06.101][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:06.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:06.102][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:06.104][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:06.106][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:06.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:06.108][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 14:04:06.110][biodb::testThat]
biodb.INFO [2024-10-17 14:04:06.111][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-10-17 14:04:06.112][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:06.114][biodb::testThat]
biodb.ERROR[2024-10-17 14:04:06.133][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-10-17 14:04:06.163][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-10-17 14:04:06.180][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 14:04:06.184][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-17 14:04:06.185][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-17 14:04:06.186][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 14:04:06.187][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.189][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.192][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 14:04:06.207][biodb::testContext]
biodb.INFO [2024-10-17 14:04:06.208][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:06.209][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-10-17 14:04:06.210][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:06.211][biodb::testContext]
biodb.INFO [2024-10-17 14:04:06.213][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:06.215][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:06.222][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:06.224][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 14:04:06.226][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 14:04:06.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.229][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.DEBUG[2024-10-17 14:04:06.230][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 14:04:06.231][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 14:04:06.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.234][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 14:04:06.235][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 14:04:06.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.238][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 14:04:06.238][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 14:04:06.239][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 14:04:06.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.242][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 14:04:06.243][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 14:04:06.244][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 14:04:06.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.247][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 14:04:06.249][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 14:04:06.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.254][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 14:04:06.255][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 14:04:06.256][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 14:04:06.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.259][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 14:04:06.260][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 14:04:06.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.263][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 14:04:06.264][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 14:04:06.265][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 14:04:06.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.268][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:06.268][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 14:04:06.269][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 14:04:06.270][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 14:04:06.271][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 14:04:06.272][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 14:04:06.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.275][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 14:04:06.276][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 14:04:06.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.279][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 14:04:06.280][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 14:04:06.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.288][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 14:04:06.289][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 14:04:06.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.292][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.DEBUG[2024-10-17 14:04:06.293][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 14:04:06.294][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 14:04:06.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.297][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 14:04:06.298][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 14:04:06.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.301][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:06.302][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 14:04:06.324][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 14:04:06.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.329][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 14:04:06.330][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 14:04:06.331][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 14:04:06.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.334][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 14:04:06.336][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.337][self$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[2024-10-17 14:04:06.338][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.338][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:06.339][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.340][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.341][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.342][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.342][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:06.343][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:06.344][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.346][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 14:04:06.347][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:06.348][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.350][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.352][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:06.352][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:06.352][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:06.352][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:06.352][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:06.357][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:06.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:06.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:06.360][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:06.361][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:06.362][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:06.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.363][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.364][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:06.365][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:06.366][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.366][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.367][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 14:04:06.369][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.370][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:06.371][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.372][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:06.373][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.373][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.374][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.375][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.376][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:06.377][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:06.379][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.381][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 14:04:06.383][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:06.384][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.385][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.386][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:06.386][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:06.386][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:06.386][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:06.386][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:06.386][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:06.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:06.388][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:06.389][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:06.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:06.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:06.391][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.392][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.393][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:06.394][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:06.394][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.395][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.396][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 14:04:06.398][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.399][self$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[2024-10-17 14:04:06.400][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.400][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:06.401][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.402][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.403][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.404][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.404][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:06.406][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:06.408][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.410][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 14:04:06.411][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:06.412][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.413][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.414][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.414][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:06.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:06.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:06.417][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:06.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:06.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:06.422][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.424][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.425][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:06.426][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:06.427][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.427][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.428][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 14:04:06.430][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.431][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:06.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:06.434][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.434][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.435][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.436][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.437][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:06.438][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:06.438][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.439][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 14:04:06.440][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:06.441][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.442][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.442][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.443][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:06.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:06.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:06.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:06.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:06.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:06.451][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.452][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.453][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:06.454][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:06.454][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.455][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:06.456][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:06.457][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.500][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[2024-10-17 14:04:06.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.536][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[2024-10-17 14:04:06.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.541][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 14:04:06.542][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 14:04:06.544][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 14:04:06.546][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 14:04:06.549][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:04:06.550][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:04:06.552][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:06.553][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:06.554][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 14:04:06.556][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:04:06.557][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:06.558][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 14:04:06.560][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:06.562][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:06.564][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 14:04:06.565][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:06.567][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 14:04:06.569][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 14:04:06.570][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:04:06.572][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 14:04:06.574][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 14:04:06.575][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 14:04:06.576][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 14:04:06.577][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 14:04:06.578][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 14:04:06.579][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 14:04:06.581][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 14:04:06.582][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 14:04:06.583][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 14:04:06.584][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 14:04:06.585][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 14:04:06.587][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 14:04:06.589][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 14:04:06.591][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 14:04:06.592][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 14:04:06.593][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 14:04:06.594][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 14:04:06.596][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 14:04:06.597][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 14:04:06.599][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 14:04:06.601][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 14:04:06.603][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 14:04:06.605][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 14:04:06.606][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 14:04:06.607][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 14:04:06.609][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 14:04:06.610][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 14:04:06.612][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 14:04:06.614][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 14:04:06.615][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 14:04:06.616][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 14:04:06.618][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 14:04:06.619][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 14:04:06.620][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 14:04:06.621][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 14:04:06.622][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 14:04:06.624][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 14:04:06.625][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 14:04:06.626][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 14:04:06.627][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 14:04:06.629][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 14:04:06.631][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 14:04:06.633][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 14:04:06.635][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 14:04:06.638][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 14:04:06.640][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 14:04:06.643][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:04:06.644][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:04:06.646][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 14:04:06.647][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 14:04:06.648][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 14:04:06.649][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 14:04:06.651][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 14:04:06.652][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 14:04:06.655][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 14:04:06.657][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 14:04:06.659][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 14:04:06.660][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 14:04:06.662][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 14:04:06.663][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 14:04:06.664][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 14:04:06.665][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 14:04:06.666][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 14:04:06.667][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 14:04:06.669][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:06.670][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:06.671][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.672][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.786][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[2024-10-17 14:04:06.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:06.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.791][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[2024-10-17 14:04:06.795][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:06.797][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-17 14:04:06.799][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.801][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.802][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.802][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:06.803][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.804][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.805][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.806][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-17 14:04:06.807][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 14:04:06.807][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:06.808][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.809][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-17 14:04:06.810][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-17 14:04:06.811][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-17 14:04:06.812][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:06.813][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:06.813][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:06.813][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:06.814][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 14:04:06.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:06.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:06.816][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:06.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:06.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:06.818][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:06.819][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:04:06.819][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-17 14:04:06.820][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:06.821][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:06.822][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:06.822][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-17 14:04:06.822][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-17 14:04:06.825][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:04:06.828][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:06.830][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-17 14:04:06.831][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:04:06.832][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:04:06.834][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:04:06.837][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-17 14:04:06.838][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-17 14:04:06.839][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-17 14:04:06.841][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-17 14:04:06.842][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:06.843][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:06.845][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-17 14:04:06.845][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-17 14:04:06.847][biodb::testThat]
biodb.INFO [2024-10-17 14:04:06.848][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-10-17 14:04:06.849][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:06.849][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:06.854][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-17 14:04:06.859][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:06.860][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-17 14:04:06.861][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:06.863][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-17 14:04:06.867][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:06.870][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:06.872][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-17 14:04:06.874][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:06.876][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-17 14:04:06.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:06.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.911][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:06.915][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:06.916][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-17 14:04:06.917][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:06.919][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-17 14:04:06.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:06.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.931][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.DEBUG[2024-10-17 14:04:06.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:06.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.963][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:06.967][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:06.970][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-17 14:04:06.972][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:06.976][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-17 14:04:06.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:06.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:06.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:06.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:06.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:06.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:06.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:06.991][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:06.997][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:06.999][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-17 14:04:07.000][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:07.002][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-17 14:04:07.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:07.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.014][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[2024-10-17 14:04:07.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:07.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.028][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[2024-10-17 14:04:07.032][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:07.035][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:07.037][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-17 14:04:07.038][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:07.039][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-17 14:04:07.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:07.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.053][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:07.057][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:07.059][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-17 14:04:07.060][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:07.062][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-17 14:04:07.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:07.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.079][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:07.083][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:07.084][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-10-17 14:04:07.085][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:07.088][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-10-17 14:04:07.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:07.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 14:04:07.107][biodb::testThat]
biodb.INFO [2024-10-17 14:04:07.108][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-10-17 14:04:07.109][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:07.110][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:07.113][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:07.118][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:07.120][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64007787a4f3864bb479683766386808".
biodb.TRACE[2024-10-17 14:04:07.121][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:07.123][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content".
biodb.DEBUG[2024-10-17 14:04:07.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:07.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.144][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:07.148][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:07.150][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7547b08b3ebd50447d61026ab0af8d63".
biodb.TRACE[2024-10-17 14:04:07.153][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:07.156][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content".
biodb.DEBUG[2024-10-17 14:04:07.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:07.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 14:04:07.174][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 14:04:07.175][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-17 14:04:07.176][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-17 14:04:07.178][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 14:04:07.179][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.182][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.183][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 14:04:07.191][biodb::testContext]
biodb.INFO [2024-10-17 14:04:07.192][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:07.193][biodb::testContext] Test context - Test web services
biodb.INFO [2024-10-17 14:04:07.194][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:07.195][biodb::testContext]
biodb.INFO [2024-10-17 14:04:07.197][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:07.199][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:07.203][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:07.205][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 14:04:07.206][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.209][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 14:04:07.210][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.218][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 14:04:07.219][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.223][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 14:04:07.224][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 14:04:07.225][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 14:04:07.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.228][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 14:04:07.228][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 14:04:07.229][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.234][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 14:04:07.235][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 14:04:07.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.240][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 14:04:07.240][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 14:04:07.241][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 14:04:07.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.245][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 14:04:07.245][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.249][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 14:04:07.250][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 14:04:07.251][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.254][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:07.255][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 14:04:07.257][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 14:04:07.258][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 14:04:07.259][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 14:04:07.260][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 14:04:07.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.263][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 14:04:07.264][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 14:04:07.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.267][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 14:04:07.268][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 14:04:07.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.274][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 14:04:07.275][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 14:04:07.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.278][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 14:04:07.279][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 14:04:07.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.282][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 14:04:07.283][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 14:04:07.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.286][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:07.286][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 14:04:07.309][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 14:04:07.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.314][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 14:04:07.315][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 14:04:07.317][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 14:04:07.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.323][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 14:04:07.325][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.327][self$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[2024-10-17 14:04:07.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.329][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:07.330][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.331][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.332][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.333][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.334][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:07.335][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:07.351][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.352][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 14:04:07.353][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:07.355][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.357][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.358][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:07.358][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:07.358][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:07.358][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:07.358][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:07.359][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:07.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:07.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:07.362][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:07.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:07.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:07.364][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.365][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.366][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:07.366][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:07.367][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.368][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.369][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 14:04:07.371][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.372][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:07.373][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.373][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:07.374][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.375][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.377][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.379][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.380][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:07.381][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:07.382][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.383][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 14:04:07.384][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:07.386][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.387][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.388][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:07.388][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:07.388][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:07.388][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:07.388][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:07.389][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:07.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:07.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:07.391][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:07.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:07.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:07.393][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.394][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.395][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:07.396][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:07.397][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.397][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.398][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 14:04:07.400][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.402][self$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[2024-10-17 14:04:07.403][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.404][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:07.406][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.407][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.408][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.409][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.410][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:07.411][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:07.411][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.412][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 14:04:07.413][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:07.414][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.415][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.415][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.416][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:07.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:07.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:07.419][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:07.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:07.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:07.421][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.422][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.422][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:07.423][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:07.424][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.425][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.426][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 14:04:07.427][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.429][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:07.430][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.431][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:07.432][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.433][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.434][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.435][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.437][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:07.438][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:07.440][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.441][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 14:04:07.442][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:07.442][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.443][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.444][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.445][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:07.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:07.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:07.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:07.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:07.449][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:07.450][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.450][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.451][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:07.452][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:07.453][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.454][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:07.455][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:07.456][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.492][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[2024-10-17 14:04:07.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.539][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 14:04:07.540][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 14:04:07.541][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 14:04:07.543][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 14:04:07.544][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:04:07.545][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:04:07.547][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:07.548][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:07.549][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 14:04:07.552][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:04:07.554][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:07.555][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 14:04:07.556][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:07.558][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:07.559][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 14:04:07.560][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:07.561][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 14:04:07.563][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 14:04:07.564][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:04:07.565][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 14:04:07.567][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 14:04:07.569][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 14:04:07.571][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 14:04:07.572][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 14:04:07.573][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 14:04:07.574][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 14:04:07.576][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 14:04:07.577][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 14:04:07.578][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 14:04:07.579][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 14:04:07.581][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 14:04:07.582][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 14:04:07.583][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 14:04:07.584][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 14:04:07.585][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 14:04:07.587][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 14:04:07.588][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 14:04:07.589][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 14:04:07.590][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 14:04:07.591][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 14:04:07.592][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 14:04:07.594][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 14:04:07.595][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 14:04:07.596][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 14:04:07.597][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 14:04:07.598][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 14:04:07.601][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 14:04:07.603][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 14:04:07.605][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 14:04:07.606][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 14:04:07.608][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 14:04:07.609][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 14:04:07.610][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 14:04:07.611][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 14:04:07.613][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 14:04:07.614][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 14:04:07.615][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 14:04:07.616][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 14:04:07.618][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 14:04:07.619][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 14:04:07.620][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 14:04:07.621][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 14:04:07.624][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 14:04:07.627][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 14:04:07.628][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 14:04:07.630][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 14:04:07.631][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:04:07.632][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:04:07.633][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 14:04:07.635][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 14:04:07.636][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 14:04:07.637][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 14:04:07.638][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 14:04:07.640][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 14:04:07.641][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 14:04:07.642][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 14:04:07.643][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 14:04:07.645][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 14:04:07.646][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 14:04:07.647][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 14:04:07.650][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 14:04:07.652][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 14:04:07.654][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 14:04:07.655][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 14:04:07.657][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:07.658][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:07.659][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.660][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.701][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.DEBUG[2024-10-17 14:04:07.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.706][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[2024-10-17 14:04:07.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.716][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[2024-10-17 14:04:07.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.772][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:07.775][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-17 14:04:07.777][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.778][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.779][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.780][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:07.781][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.782][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.783][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.783][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-17 14:04:07.784][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 14:04:07.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:07.788][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.789][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-17 14:04:07.790][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-17 14:04:07.791][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-17 14:04:07.792][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:07.793][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:07.793][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:07.793][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:07.794][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 14:04:07.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:07.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:07.797][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:07.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:07.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:07.799][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:07.801][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:04:07.801][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-17 14:04:07.803][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:07.805][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:07.806][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:07.807][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-17 14:04:07.807][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-17 14:04:07.808][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:04:07.810][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:07.811][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-17 14:04:07.813][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:04:07.814][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:04:07.815][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:04:07.820][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-17 14:04:07.821][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-17 14:04:07.822][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-17 14:04:07.824][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-17 14:04:07.827][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:07.829][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:07.830][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-17 14:04:07.832][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-17 14:04:07.835][biodb::testThat]
biodb.INFO [2024-10-17 14:04:07.836][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-10-17 14:04:07.837][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:07.839][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:07.844][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-17 14:04:07.848][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:07.849][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-17 14:04:07.850][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:07.852][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-17 14:04:07.856][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:07.859][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:07.861][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-10-17 14:04:07.862][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:07.864][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.INFO [2024-10-17 14:04:07.876][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 14:04:07.878][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-17 14:04:07.879][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-17 14:04:07.880][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 14:04:07.881][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:07.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:07.885][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:07.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:07.890][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 14:04:07.895][biodb::testContext]
biodb.INFO [2024-10-17 14:04:07.896][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:07.897][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-10-17 14:04:07.898][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 14:04:07.899][biodb::testContext]
biodb.INFO [2024-10-17 14:04:07.901][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:07.903][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:07.907][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:07.909][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 14:04:07.911][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.915][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[2024-10-17 14:04:07.915][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 14:04:07.916][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.920][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 14:04:07.921][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.926][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 14:04:07.927][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 14:04:07.928][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 14:04:07.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.932][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 14:04:07.933][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 14:04:07.933][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.937][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 14:04:07.937][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 14:04:07.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.940][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 14:04:07.941][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 14:04:07.942][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 14:04:07.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.947][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 14:04:07.949][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.956][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 14:04:07.957][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 14:04:07.958][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 14:04:07.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.961][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:07.962][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 14:04:07.963][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 14:04:07.964][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 14:04:07.964][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 14:04:07.965][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 14:04:07.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.968][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 14:04:07.969][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 14:04:07.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.971][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[2024-10-17 14:04:07.972][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 14:04:07.973][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 14:04:07.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.976][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 14:04:07.977][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 14:04:07.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.982][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[2024-10-17 14:04:07.984][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 14:04:07.985][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 14:04:07.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:07.988][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 14:04:07.989][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 14:04:07.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:07.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:07.991][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[2024-10-17 14:04:07.992][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 14:04:07.993][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 14:04:08.017][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 14:04:08.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.022][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 14:04:08.023][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 14:04:08.025][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 14:04:08.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.031][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 14:04:08.032][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.033][self$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[2024-10-17 14:04:08.034][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.035][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:08.036][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.037][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.038][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.040][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.041][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:08.042][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:08.043][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.044][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 14:04:08.045][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:08.047][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.049][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.050][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:08.050][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:08.050][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:08.050][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:08.050][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:08.051][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:08.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:08.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:08.055][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:08.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:08.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:08.057][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.058][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:08.061][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:08.062][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.064][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.066][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 14:04:08.070][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.071][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:08.072][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.073][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:08.074][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.074][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.075][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.084][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.085][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:08.086][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:08.087][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.088][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 14:04:08.088][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:08.090][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.092][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.093][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:08.093][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:08.093][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:08.093][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 14:04:08.093][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 14:04:08.095][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:08.096][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:08.097][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:08.098][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:08.099][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:08.099][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:08.100][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.101][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.102][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:08.103][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:08.104][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.105][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.106][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 14:04:08.107][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.108][self$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[2024-10-17 14:04:08.109][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.110][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:08.111][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.112][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.112][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.113][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.114][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 14:04:08.115][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:08.116][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.116][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 14:04:08.117][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:08.118][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.119][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.120][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.121][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:08.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:08.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:08.124][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:08.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:08.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:08.128][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.129][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.130][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:08.131][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:08.132][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.133][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.134][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 14:04:08.136][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.137][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 14:04:08.138][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.139][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:08.140][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.141][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.142][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.142][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.143][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 14:04:08.144][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:08.145][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.146][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 14:04:08.148][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:08.149][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.150][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.152][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.152][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 14:04:08.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:08.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:08.155][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:08.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:08.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:08.157][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.158][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.159][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:08.159][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:08.160][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.161][self$setPropertyValue]
biodb.DEBUG[2024-10-17 14:04:08.162][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:08.163][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.164][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[2024-10-17 14:04:08.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.174][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[2024-10-17 14:04:08.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.178][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[2024-10-17 14:04:08.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.200][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.DEBUG[2024-10-17 14:04:08.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.225][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[2024-10-17 14:04:08.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.228][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[2024-10-17 14:04:08.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.238][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.DEBUG[2024-10-17 14:04:08.240][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 14:04:08.242][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 14:04:08.243][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 14:04:08.244][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 14:04:08.246][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:04:08.247][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 14:04:08.248][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:08.250][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:08.251][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 14:04:08.252][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 14:04:08.254][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:08.255][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 14:04:08.257][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 14:04:08.258][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 14:04:08.259][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 14:04:08.261][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 14:04:08.263][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 14:04:08.265][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 14:04:08.267][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:04:08.269][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 14:04:08.271][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 14:04:08.273][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 14:04:08.274][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 14:04:08.276][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 14:04:08.277][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 14:04:08.278][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 14:04:08.279][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 14:04:08.281][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 14:04:08.282][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 14:04:08.283][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 14:04:08.284][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 14:04:08.285][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 14:04:08.287][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 14:04:08.290][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 14:04:08.292][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 14:04:08.293][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 14:04:08.295][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 14:04:08.296][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 14:04:08.297][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 14:04:08.298][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 14:04:08.299][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 14:04:08.301][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 14:04:08.302][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 14:04:08.303][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 14:04:08.304][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 14:04:08.306][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 14:04:08.307][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 14:04:08.308][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 14:04:08.309][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 14:04:08.310][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 14:04:08.312][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 14:04:08.313][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 14:04:08.314][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 14:04:08.315][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 14:04:08.316][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 14:04:08.317][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 14:04:08.319][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 14:04:08.320][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 14:04:08.321][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 14:04:08.322][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 14:04:08.323][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 14:04:08.324][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 14:04:08.326][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 14:04:08.327][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 14:04:08.328][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 14:04:08.329][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 14:04:08.330][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:04:08.332][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:04:08.333][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 14:04:08.334][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 14:04:08.335][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 14:04:08.338][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 14:04:08.340][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 14:04:08.342][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 14:04:08.343][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 14:04:08.344][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 14:04:08.346][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 14:04:08.347][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 14:04:08.348][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 14:04:08.349][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 14:04:08.351][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 14:04:08.352][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 14:04:08.353][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 14:04:08.354][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 14:04:08.356][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 14:04:08.357][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 14:04:08.358][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.361][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.362][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[2024-10-17 14:04:08.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.369][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[2024-10-17 14:04:08.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.385][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[2024-10-17 14:04:08.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.392][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[2024-10-17 14:04:08.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.419][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[2024-10-17 14:04:08.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 14:04:08.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 14:04:08.468][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-17 14:04:08.471][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-17 14:04:08.474][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.475][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.476][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.477][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 14:04:08.478][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.480][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.481][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.482][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-17 14:04:08.483][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 14:04:08.484][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 14:04:08.485][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.486][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-17 14:04:08.487][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-17 14:04:08.488][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-17 14:04:08.489][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 14:04:08.490][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 14:04:08.490][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 14:04:08.490][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 14:04:08.490][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 14:04:08.491][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:08.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:08.493][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 14:04:08.494][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 14:04:08.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 14:04:08.495][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 14:04:08.496][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 14:04:08.496][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-17 14:04:08.497][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 14:04:08.498][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 14:04:08.498][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 14:04:08.499][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-17 14:04:08.499][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-17 14:04:08.500][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 14:04:08.502][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 14:04:08.503][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-17 14:04:08.504][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 14:04:08.506][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 14:04:08.509][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 14:04:08.515][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-17 14:04:08.517][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-17 14:04:08.518][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-17 14:04:08.519][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-17 14:04:08.520][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:08.521][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 14:04:08.522][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-17 14:04:08.523][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-17 14:04:08.525][biodb::testThat]
biodb.INFO [2024-10-17 14:04:08.526][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-10-17 14:04:08.526][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 14:04:08.527][biodb::testThat]
biodb.DEBUG[2024-10-17 14:04:08.530][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-17 14:04:08.534][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:08.535][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-17 14:04:08.537][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:08.538][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-17 14:04:08.542][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 14:04:08.547][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 14:04:08.549][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-10-17 14:04:08.551][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:08.552][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-10-17 14:04:08.558][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-10-17 14:04:08.559][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 14:04:08.561][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-10-17 14:04:08.563][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 14:04:08.565][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml".
biodb.DEBUG[2024-10-17 14:04:08.569][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 14:04:08.571][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 14:04:08.572][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 14:04:08.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 14:04:08.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 14:04:08.592][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:08.593][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:08.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.596][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:08.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:08.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.603][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:08.604][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:08.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.607][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.609][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 14:04:08.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 14:04:08.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.612][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:08.613][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:08.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.615][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.616][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 14:04:08.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 14:04:08.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.620][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 14:04:08.620][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 14:04:08.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.622][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.623][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 14:04:08.624][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 14:04:08.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.626][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.627][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:08.628][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:08.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.629][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.631][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:08.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 14:04:08.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.636][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:08.638][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:08.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.640][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.641][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 14:04:08.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 14:04:08.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.645][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:08.646][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:08.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.648][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:08.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 14:04:08.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.652][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:08.653][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:08.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.655][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 14:04:08.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 14:04:08.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.660][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:08.661][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:08.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.662][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.664][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 14:04:08.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 14:04:08.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.667][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:08.668][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:08.669][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.670][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.672][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 14:04:08.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 14:04:08.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:08.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:08.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:08.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:08.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:08.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:08.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 14:04:08.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 14:04:08.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:08.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:08.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:08.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:08.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:08.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:08.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:08.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:08.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:08.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:08.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 14:04:08.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 14:04:08.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 14:04:08.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 14:04:08.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 14:04:08.719][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-10-17 14:04:08.724][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 14:04:08.725][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-17 14:04:08.727][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-17 14:04:08.728][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 14:04:08.729][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 14:04:08.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 14:04:08.731][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 14:04:08.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 14:04:08.733][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 14:04:08.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 381 ]
> 
> proc.time()
   user  system elapsed 
 18.605   1.267  24.252

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.6520.7093.807
ChebiEntry0.4540.0220.488