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This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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: 2024-06-23 14:00 -0400 (Sun, 23 Jun 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbChebi on kjohnson1

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

raw results


Summary

Package: biodbChebi
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.10.0.tar.gz
StartedAt: 2024-06-24 12:42:02 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 12:43:20 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 78.5 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 4.4.0 (2024-04-24)
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-06-24 12:42:49.632][biodb::testContext]
biodb.INFO [2024-06-24 12:42:49.638][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:42:49.639][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-24 12:42:49.640][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:42:49.641][biodb::testContext]
biodb.INFO [2024-06-24 12:42:49.650][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:42:49.653][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 12:42:49.663][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:42:49.665][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 12:42:49.666][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 12:42:49.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.670][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 12:42:49.692][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 12:42:49.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.696][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 12:42:49.697][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 12:42:49.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.700][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 12:42:49.701][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 12:42:49.702][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 12:42:49.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.722][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 12:42:49.723][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 12:42:49.724][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 12:42:49.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.727][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 12:42:49.728][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 12:42:49.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.731][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 12:42:49.732][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 12:42:49.733][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 12:42:49.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.736][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 12:42:49.736][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 12:42:49.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.739][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 12:42:49.740][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 12:42:49.741][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 12:42:49.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.744][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:42:49.745][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 12:42:49.746][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 12:42:49.746][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 12:42:49.747][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 12:42:49.748][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 12:42:49.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.751][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 12:42:49.752][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 12:42:49.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.755][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 12:42:49.756][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 12:42:49.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.759][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 12:42:49.760][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 12:42:49.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.763][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 12:42:49.764][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 12:42:49.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.767][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 12:42:49.768][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 12:42:49.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.772][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:42:49.773][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 12:42:49.790][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 12:42:49.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.793][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 12:42:49.794][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 12:42:49.795][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 12:42:49.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.803][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 12:42:49.839][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.856][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 12:42:49.857][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.859][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:42:49.860][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.861][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.862][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.862][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.863][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:42:49.864][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:42:49.865][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.866][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 12:42:49.867][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:42:49.868][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.869][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.870][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:42:49.870][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:42:49.870][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:42:49.870][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:42:49.870][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:42:49.871][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:42:49.872][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:42:49.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:42:49.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:42:49.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:42:49.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:42:49.876][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.877][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.877][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:42:49.878][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:42:49.879][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.880][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.881][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 12:42:49.883][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.884][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:42:49.885][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.886][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:42:49.886][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.887][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.888][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.889][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.890][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:42:49.891][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:42:49.892][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.893][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 12:42:49.894][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:42:49.895][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.896][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.897][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:42:49.897][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:42:49.897][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:42:49.897][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:42:49.897][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:42:49.898][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:42:49.899][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:42:49.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:42:49.901][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:42:49.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:42:49.903][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:42:49.904][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.905][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.906][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:42:49.906][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:42:49.907][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.908][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.909][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 12:42:49.911][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.912][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 12:42:49.912][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.913][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:42:49.914][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.915][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.916][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.917][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.918][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:42:49.925][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:42:49.927][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.928][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 12:42:49.929][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:42:49.929][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.930][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.931][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.932][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:42:49.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:42:49.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:42:49.934][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:42:49.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:42:49.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:42:49.937][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.938][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.939][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:42:49.939][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:42:49.940][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.941][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.942][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 12:42:49.944][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.945][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:42:49.946][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.947][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:42:49.948][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.949][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.950][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.951][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.952][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:42:49.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:42:49.954][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.954][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 12:42:49.955][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:42:49.956][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.957][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:49.958][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.959][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:42:49.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:42:49.960][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:42:49.961][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:42:49.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:42:49.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:42:49.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:42:49.964][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.965][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:42:49.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:42:49.967][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:49.968][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:42:49.973][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:42:49.980][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:49.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:49.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.985][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.DEBUG[2024-06-24 12:42:49.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:49.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:49.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:49.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:49.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.992][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[2024-06-24 12:42:49.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:49.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:49.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:49.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:49.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:49.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:49.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:49.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.048][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 12:42:50.054][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 12:42:50.056][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 12:42:50.057][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 12:42:50.059][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:42:50.060][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:42:50.062][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 12:42:50.063][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 12:42:50.064][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 12:42:50.066][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:42:50.067][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:42:50.068][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 12:42:50.069][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 12:42:50.070][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 12:42:50.071][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 12:42:50.072][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:42:50.074][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 12:42:50.076][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 12:42:50.078][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:42:50.079][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 12:42:50.080][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 12:42:50.081][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 12:42:50.083][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 12:42:50.085][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 12:42:50.086][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 12:42:50.087][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 12:42:50.090][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 12:42:50.091][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 12:42:50.093][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 12:42:50.096][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 12:42:50.097][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 12:42:50.099][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 12:42:50.101][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 12:42:50.103][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 12:42:50.104][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 12:42:50.105][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 12:42:50.107][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 12:42:50.108][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 12:42:50.110][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 12:42:50.112][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 12:42:50.113][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 12:42:50.115][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 12:42:50.116][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 12:42:50.118][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 12:42:50.127][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 12:42:50.129][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 12:42:50.130][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 12:42:50.133][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 12:42:50.135][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 12:42:50.136][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 12:42:50.138][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 12:42:50.140][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 12:42:50.145][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 12:42:50.147][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 12:42:50.155][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 12:42:50.162][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 12:42:50.166][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 12:42:50.167][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 12:42:50.168][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 12:42:50.169][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 12:42:50.171][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 12:42:50.172][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 12:42:50.173][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 12:42:50.174][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 12:42:50.175][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 12:42:50.176][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 12:42:50.178][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:42:50.179][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:42:50.180][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 12:42:50.181][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 12:42:50.182][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 12:42:50.184][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 12:42:50.185][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 12:42:50.186][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 12:42:50.187][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 12:42:50.188][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 12:42:50.189][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 12:42:50.190][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 12:42:50.192][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 12:42:50.193][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 12:42:50.194][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 12:42:50.195][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 12:42:50.196][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 12:42:50.202][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 12:42:50.204][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:42:50.208][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:42:50.209][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.211][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.221][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[2024-06-24 12:42:50.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.235][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.DEBUG[2024-06-24 12:42:50.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.240][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.DEBUG[2024-06-24 12:42:50.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.271][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[2024-06-24 12:42:50.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.286][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[2024-06-24 12:42:50.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:42:50.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:50.304][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 12:42:50.320][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 12:42:50.323][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:50.324][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 12:42:50.325][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:50.326][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:42:50.327][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:50.327][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:42:50.328][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:50.329][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 12:42:50.330][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 12:42:50.331][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:42:50.331][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:50.332][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 12:42:50.333][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 12:42:50.334][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 12:42:50.335][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 12:42:50.336][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:42:50.336][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:42:50.336][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:42:50.337][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 12:42:50.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:42:50.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:42:50.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:42:50.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:42:50.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:42:50.342][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:42:50.343][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:50.343][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 12:42:50.344][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:42:50.345][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:42:50.346][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 12:42:50.346][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 12:42:50.346][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 12:42:50.354][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:42:50.356][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:42:50.357][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 12:42:50.358][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:42:50.360][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:42:50.361][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:42:50.393][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 12:42:50.395][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 12:42:50.400][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 12:42:50.406][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 12:42:50.411][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:42:50.412][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:42:50.414][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 12:42:50.415][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 12:42:50.428][biodb::testThat]
biodb.INFO [2024-06-24 12:42:50.429][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-24 12:42:50.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:42:50.431][biodb::testThat]
biodb.TRACE[2024-06-24 12:42:50.437][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-06-24 12:42:50.440][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:50.444][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:50.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:50.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:50.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:50.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:50.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:50.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:50.475][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.TRACE[2024-06-24 12:42:50.487][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.488][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.490][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.509][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:50.510][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:50.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.511][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.539][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:50.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:50.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.543][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:50.544][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:50.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.545][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.547][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:50.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:50.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.550][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:50.564][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:50.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.566][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:50.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:50.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.570][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:50.571][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:50.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.573][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:50.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:50.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.579][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:50.580][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:50.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.581][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.582][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:50.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:50.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.586][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:50.587][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:50.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.588][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.590][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:50.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:50.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.593][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:50.594][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:50.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.596][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:50.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:50.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.600][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:50.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:50.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.603][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:50.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:50.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.609][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:50.610][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:50.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.611][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.612][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:50.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:50.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.616][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:50.617][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:50.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.618][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:50.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:50.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:50.691][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-06-24 12:42:50.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:50.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:50.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:50.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:50.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:50.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:50.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:50.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:50.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:50.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:50.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:50.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:50.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:42:50.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:42:50.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:42:50.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:42:50.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.797][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:42:50.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:42:50.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.801][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:42:50.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:42:50.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.912][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.913][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.915][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:50.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:50.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.948][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.949][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.950][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:50.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:50.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:50.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:50.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:50.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:50.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:50.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.975][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:50.976][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:50.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.978][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:50.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:50.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.991][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:50.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:50.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:50.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:50.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:50.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:50.999][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:51.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:51.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.003][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:51.004][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:51.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.005][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.006][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:51.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:51.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.029][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.030][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.031][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.055][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.056][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.057][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.070][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:51.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:51.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.074][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:51.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:51.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.078][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:51.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:51.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.082][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:51.089][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:51.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.092][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.092][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:51.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:51.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.104][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.108][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.112][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.116][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.117][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.119][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.120][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.134][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.138][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.141][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.145][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.146][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.147][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.148][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.160][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:51.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:51.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.165][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:51.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:51.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.170][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:51.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:51.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.174][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:51.175][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:51.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.176][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.177][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:51.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:51.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.200][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.201][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.202][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.203][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:51.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:51.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:51.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:51.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:51.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:51.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.226][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:51.227][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:51.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.229][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.229][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:51.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:51.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.241][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:51.242][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:51.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.244][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.249][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:51.257][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:51.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.259][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.265][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:51.267][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:51.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.268][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.274][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:51.275][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:51.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.276][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.282][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.283][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.284][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.289][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.291][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.292][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.297][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.298][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.300][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.304][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.305][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.307][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.312][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.313][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.314][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.319][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:51.320][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:51.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.321][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.326][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:51.328][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:51.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.329][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:42:51.337][biodb::testThat]
biodb.INFO [2024-06-24 12:42:51.338][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-24 12:42:51.339][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:42:51.340][biodb::testThat]
biodb.DEBUG[2024-06-24 12:42:51.354][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-06-24 12:42:51.364][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:51.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-06-24 12:42:51.370][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:42:51.372][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-06-24 12:42:51.373][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:51.396][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:51.398][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:51.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:51.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:51.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:51.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:51.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:51.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:51.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:51.412][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:51.413][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:51.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.414][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:51.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:51.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.444][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:51.445][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:51.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.447][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.448][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:51.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:51.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.452][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:51.453][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:51.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.454][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.455][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:51.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:51.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.459][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:51.460][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:51.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.461][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:51.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:51.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.466][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.467][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.468][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:51.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.473][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.474][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.476][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.477][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:51.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.480][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:51.481][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.483][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.484][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:51.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:51.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.489][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.490][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.492][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:51.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.497][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:51.498][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:51.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.500][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:51.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:51.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.505][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:51.506][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.508][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.509][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:51.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:51.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.512][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:51.513][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:51.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.515][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.516][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:51.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:51.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:51.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:51.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:51.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:51.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:51.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:51.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:51.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:51.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:51.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:51.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:51.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:51.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:51.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:51.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:51.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:51.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:51.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:51.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:51.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:51.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:51.553][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-06-24 12:42:51.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-24 12:42:51.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-24 12:42:51.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-24 12:42:51.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-24 12:42:51.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-24 12:42:51.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-24 12:42:51.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:42:51.578][biodb::testThat]
biodb.INFO [2024-06-24 12:42:51.579][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-24 12:42:51.580][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:42:51.581][biodb::testThat]
biodb.TRACE[2024-06-24 12:42:51.584][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:51.585][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:51.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.587][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:51.588][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-06-24 12:42:51.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:51.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:51.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:51.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:51.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:51.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:51.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:51.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:51.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:51.631][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-06-24 12:42:51.637][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 12:42:51.658][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:42:51.673][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-24 12:42:51.675][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:42:51.676][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-24 12:42:51.699][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:42:51.703][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:51.704][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:51.705][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:42:52.043][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:42:52.257][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:52.260][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-06-24 12:42:52.277][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-06-24 12:42:52.280][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-06-24 12:42:52.295][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:52.297][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:52.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.298][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.299][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:52.300][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:52.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.318][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:42:52.324][biodb::testThat]
biodb.INFO [2024-06-24 12:42:52.325][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-24 12:42:52.326][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:42:52.326][biodb::testThat]
biodb.TRACE[2024-06-24 12:42:52.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:52.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:52.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:52.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:52.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:52.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:52.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:52.421][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:42:52.425][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:42:52.427][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 12:42:52.428][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:42:52.430][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-06-24 12:42:52.456][biodb::testThat]
biodb.INFO [2024-06-24 12:42:52.457][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-24 12:42:52.458][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:42:52.458][biodb::testThat]
biodb.TRACE[2024-06-24 12:42:52.481][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:52.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:52.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:52.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:52.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:52.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:52.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:52.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:52.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:52.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:52.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:52.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:52.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.502][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:42:52.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:42:52.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.505][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:42:52.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:42:52.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.508][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:42:52.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:42:52.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.511][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:42:52.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:42:52.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:52.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:52.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:52.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:52.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:52.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:52.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:52.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:52.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:52.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:52.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:52.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:52.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.554][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:42:52.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:42:52.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-24 12:42:52.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-24 12:42:52.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.569][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-24 12:42:52.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-24 12:42:52.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:52.572][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-24 12:42:52.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-24 12:42:52.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:52.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:42:52.583][biodb::testThat]
biodb.INFO [2024-06-24 12:42:52.585][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-24 12:42:52.585][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:42:52.586][biodb::testThat]
biodb.INFO [2024-06-24 12:42:52.596][biodb::testThat]
biodb.INFO [2024-06-24 12:42:52.597][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-24 12:42:52.598][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:42:52.599][biodb::testThat]
biodb.INFO [2024-06-24 12:42:52.608][biodb::testThat]
biodb.INFO [2024-06-24 12:42:52.609][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-24 12:42:52.610][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:42:52.611][biodb::testThat]
biodb.DEBUG[2024-06-24 12:42:52.615][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-06-24 12:42:52.804][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-06-24 12:42:53.061][biodb::testThat]
biodb.INFO [2024-06-24 12:42:53.062][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-24 12:42:53.063][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:42:53.064][biodb::testThat]
biodb.DEBUG[2024-06-24 12:42:53.174][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-06-24 12:42:53.285][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:53.287][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:53.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.289][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:53.290][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:53.291][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:53.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.292][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:42:53.294][biodb::testThat]
biodb.INFO [2024-06-24 12:42:53.295][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-24 12:42:53.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:42:53.297][biodb::testThat]
biodb.TRACE[2024-06-24 12:42:53.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:53.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:53.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:53.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:53.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:53.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:53.318][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:53.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:53.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:53.417][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:42:53.420][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:42:53.422][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 12:42:53.424][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:42:53.425][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 12:42:53.499][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:42:53.502][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:42:53.504][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 12:42:53.505][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:42:53.507][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-06-24 12:42:53.522][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:42:53.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:42:53.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:53.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:53.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:53.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:53.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:53.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:53.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:53.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:53.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:53.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:53.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:53.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:53.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:53.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:53.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:53.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:53.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:53.559][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:42:53.576][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:53.577][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:53.600][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:42:53.675][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:42:53.746][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:53.749][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-24 12:42:53.754][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-24 12:42:53.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:53.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:53.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:53.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:53.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:53.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:53.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:53.768][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-06-24 12:42:53.815][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:53.817][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-06-24 12:42:53.818][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:53.819][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:53.820][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:53.821][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:53.822][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:53.823][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:53.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:53.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:53.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:53.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:53.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:53.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:53.836][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.DEBUG[2024-06-24 12:42:53.837][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-06-24 12:42:53.840][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:53.841][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:53.842][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-06-24 12:42:53.919][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-06-24 12:42:54.002][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:54.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-06-24 12:42:54.010][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-06-24 12:42:54.013][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-06-24 12:42:54.015][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:54.016][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:54.017][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:54.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:54.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:54.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:54.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:54.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:54.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:54.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:54.031][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.032][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.034][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.039][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:54.040][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:54.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.041][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.043][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:54.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:54.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.046][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:54.047][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:54.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.049][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.050][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:54.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:54.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.055][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:54.056][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:54.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.057][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:54.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:54.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.062][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:54.063][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:54.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.064][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:54.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:54.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.069][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:54.070][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:54.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.071][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.073][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:54.074][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.075][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.076][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:54.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.080][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:54.081][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:54.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.082][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:54.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:54.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.087][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:54.088][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:54.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.089][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:54.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:54.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.094][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:54.095][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:54.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.096][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.098][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:54.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:54.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.101][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:54.103][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:54.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.104][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.105][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:54.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:54.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:54.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:54.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:54.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:54.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:54.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:54.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:54.152][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-06-24 12:42:54.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:54.173][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:42:54.176][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:54.177][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:54.179][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:42:54.253][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:42:54.321][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:54.324][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-24 12:42:54.328][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-24 12:42:54.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:54.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:54.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:54.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:54.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:54.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:54.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:54.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:54.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:54.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:54.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:54.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:54.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:54.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:54.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:54.389][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-06-24 12:42:54.390][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:54.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-06-24 12:42:54.394][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:54.396][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:54.397][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:54.398][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:54.399][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:54.400][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:54.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:54.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:54.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:54.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:54.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:54.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:54.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:54.427][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-06-24 12:42:54.430][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:54.431][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:42:54.432][rule$waitAsNeeded] Wait 0.160134 second(s).
biodb.TRACE[2024-06-24 12:42:54.744][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-06-24 12:42:54.820][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-06-24 12:42:54.895][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:54.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-06-24 12:42:54.902][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-06-24 12:42:54.904][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-06-24 12:42:54.906][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:54.907][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:54.908][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:54.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:54.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:54.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:54.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:54.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:54.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:54.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:54.922][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.923][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.924][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:54.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:54.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.929][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:54.930][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:54.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.931][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.932][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:54.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:54.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.936][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:54.936][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:54.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.949][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.950][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:54.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:54.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.954][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:54.955][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:54.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.956][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:54.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:54.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.960][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:54.961][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:54.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.963][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:54.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:54.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.967][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:54.968][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:54.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.971][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:54.972][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.973][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.974][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:54.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:54.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.978][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:54.978][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:54.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.980][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:54.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:54.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.984][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:54.985][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:54.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.987][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:54.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:54.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.994][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:54.995][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:54.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:54.996][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:54.997][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:54.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:54.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.001][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:55.002][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:55.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.003][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.004][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:55.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:55.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:55.042][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-06-24 12:42:55.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:55.079][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:42:55.082][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:42:55.084][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 12:42:55.085][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:42:55.086][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 12:42:55.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:55.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:55.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:55.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:55.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:55.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:55.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:55.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:55.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:55.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:55.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:55.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:55.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:55.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:55.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:55.121][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-06-24 12:42:55.122][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:55.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-06-24 12:42:55.125][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:55.126][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:55.127][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:55.128][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:55.129][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:55.129][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:55.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:55.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:55.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:55.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:55.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:55.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:55.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:55.143][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-06-24 12:42:55.146][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:55.146][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:55.148][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-06-24 12:42:55.224][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-06-24 12:42:55.296][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:55.299][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-06-24 12:42:55.303][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-06-24 12:42:55.306][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-06-24 12:42:55.308][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:55.309][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:55.320][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:55.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:55.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:55.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:55.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:55.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:55.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:55.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:55.335][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.336][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.338][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.343][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:55.344][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:55.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.345][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.346][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:55.347][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:55.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.349][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.350][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:55.351][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:55.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.353][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.354][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:55.355][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:55.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.356][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.357][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:55.358][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:55.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.360][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.361][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:55.363][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.365][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.366][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:55.368][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:55.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.369][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.370][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:55.371][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:55.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.373][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:55.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:55.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.378][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:55.378][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:55.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.380][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:55.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:55.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.385][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:55.386][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:55.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.387][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:55.430][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-06-24 12:42:55.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:55.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:55.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:55.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:55.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:55.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:55.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:55.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:55.463][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-06-24 12:42:55.464][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:55.465][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-06-24 12:42:55.467][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:55.468][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:55.470][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:55.471][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:55.472][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:55.473][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:55.477][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:55.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:55.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:55.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:55.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:55.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:55.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:55.491][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-06-24 12:42:55.495][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:55.496][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:55.498][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-06-24 12:42:55.573][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-06-24 12:42:55.647][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:55.650][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-06-24 12:42:55.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-06-24 12:42:55.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-06-24 12:42:55.659][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:55.660][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:55.662][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:55.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:55.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:55.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:55.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:55.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:55.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:55.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:55.676][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.677][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.679][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.683][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:55.684][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:55.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.686][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.687][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:55.688][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:55.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.690][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.692][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:55.693][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:55.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.695][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.696][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:55.697][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:55.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.710][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.711][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:55.712][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:55.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.714][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.715][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:55.716][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.718][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.719][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:55.720][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:55.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.721][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.723][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:55.724][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:55.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.725][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:55.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:55.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.731][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:55.732][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:55.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.733][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.734][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:55.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:55.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.738][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:55.739][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:55.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.741][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:55.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:55.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:55.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:55.776][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-06-24 12:42:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:55.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:55.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:55.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:55.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:55.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:55.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:55.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:55.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:55.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:55.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:55.806][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-06-24 12:42:55.847][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:55.849][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-06-24 12:42:55.850][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:55.851][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:55.852][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:55.853][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:55.854][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:55.855][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:55.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:55.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:55.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:55.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:55.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:55.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:55.868][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[2024-06-24 12:42:55.869][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-06-24 12:42:55.873][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:55.874][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:55.876][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-06-24 12:42:55.949][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-06-24 12:42:56.022][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:56.024][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-06-24 12:42:56.028][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-06-24 12:42:56.031][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-06-24 12:42:56.032][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:56.034][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:56.035][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:56.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:56.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:56.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:56.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:56.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:56.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:56.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:56.049][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.050][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.051][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.056][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:56.057][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:56.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.058][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.059][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:56.060][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:56.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.062][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.063][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:56.064][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:56.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.065][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.066][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:56.067][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:56.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.069][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.070][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:56.070][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:56.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.072][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.073][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:56.074][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.075][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.076][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:56.077][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:56.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.079][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.080][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:56.081][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:56.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.082][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:56.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:56.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.087][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:56.088][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:56.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.090][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.091][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:56.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:56.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.094][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:56.095][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:56.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.096][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:56.141][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-06-24 12:42:56.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:56.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:56.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:56.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:56.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:56.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:56.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:56.169][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[2024-06-24 12:42:56.170][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-06-24 12:42:56.171][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:56.173][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-06-24 12:42:56.175][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:56.176][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:56.176][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:56.177][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:56.178][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:56.179][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:56.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:56.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:56.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:56.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:56.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:56.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:56.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:56.193][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-06-24 12:42:56.197][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:56.198][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:56.199][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-06-24 12:42:56.267][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-06-24 12:42:56.345][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:56.347][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-06-24 12:42:56.351][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-06-24 12:42:56.354][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-06-24 12:42:56.356][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:56.367][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:56.369][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:56.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:56.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:56.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:56.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:56.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:56.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:56.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:56.383][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.385][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.386][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.391][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:56.392][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:56.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.393][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.394][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:56.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:56.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.398][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:56.399][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:56.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.400][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.402][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:56.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:56.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.405][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:56.406][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:56.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.407][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.408][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:56.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:56.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.412][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:56.413][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:56.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.414][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:56.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:56.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.418][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:56.419][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:56.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.421][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.422][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:56.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:56.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.425][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:56.426][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.427][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.428][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:56.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.432][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:56.433][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:56.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.434][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:56.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:56.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.438][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:56.439][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:56.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.441][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:56.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:56.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.445][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:56.446][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:56.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.448][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.449][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:56.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:56.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.452][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:56.453][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:56.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.454][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.455][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:56.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:56.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:56.499][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-06-24 12:42:56.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:56.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:56.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:56.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:56.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:56.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:56.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:56.519][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.DEBUG[2024-06-24 12:42:56.520][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-06-24 12:42:56.521][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:56.522][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-06-24 12:42:56.524][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:56.525][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:56.526][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:56.526][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:56.527][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:56.528][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:56.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:56.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:56.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:56.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:56.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:56.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:56.541][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[2024-06-24 12:42:56.542][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-06-24 12:42:56.545][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:56.546][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:56.547][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-06-24 12:42:56.618][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-06-24 12:42:56.688][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:56.691][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-06-24 12:42:56.694][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-06-24 12:42:56.697][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-06-24 12:42:56.699][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:56.701][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:56.702][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:56.704][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:56.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:56.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:56.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:56.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:56.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:56.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:56.726][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.728][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.730][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.735][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:56.736][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:56.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.737][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.738][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:56.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:56.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.742][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:56.743][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:56.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.744][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.746][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:56.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:56.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.749][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:56.750][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:56.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.752][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:56.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:56.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.756][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:56.757][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:56.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.758][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:56.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:56.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.763][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:56.764][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:56.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.765][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.766][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:56.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:56.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.770][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:56.771][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.772][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.773][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:56.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.777][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:56.777][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:56.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.779][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:56.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:56.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.783][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:56.784][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:56.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.786][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:56.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:56.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.791][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:56.792][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:56.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.793][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.794][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:56.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:56.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.798][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:56.799][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:56.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.800][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.801][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:56.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:56.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:56.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:56.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:56.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:56.845][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-06-24 12:42:56.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:56.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:56.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:56.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:56.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:56.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:56.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:56.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:56.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:56.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:56.866][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[2024-06-24 12:42:56.867][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-06-24 12:42:56.868][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:56.869][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-06-24 12:42:56.870][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:56.871][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:56.872][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:56.873][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:56.874][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:56.875][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:56.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:56.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:56.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:56.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:56.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:56.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:56.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:56.888][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-06-24 12:42:56.890][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:56.891][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:56.893][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-06-24 12:42:56.966][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-06-24 12:42:57.037][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:57.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-06-24 12:42:57.044][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-06-24 12:42:57.046][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-06-24 12:42:57.048][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:57.049][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:57.050][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:57.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:57.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:57.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:57.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:57.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:57.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:57.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:57.064][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.065][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.066][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.071][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:57.072][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:57.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.073][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.074][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:57.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:57.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.089][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:57.090][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:57.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.091][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.093][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:57.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:57.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.096][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:57.097][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:57.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.098][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:57.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:57.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.103][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.104][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.105][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.110][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:57.110][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:57.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.112][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.113][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:57.114][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.115][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.116][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:57.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.120][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.121][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.122][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.126][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:57.127][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:57.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.129][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.130][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:57.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:57.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.133][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:57.134][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:57.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.136][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.137][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:57.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:57.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.140][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:57.141][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:57.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.143][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.144][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:57.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:57.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:57.188][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-06-24 12:42:57.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:57.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:57.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:57.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:57.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:57.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:57.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:57.208][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[2024-06-24 12:42:57.209][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-06-24 12:42:57.209][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:57.211][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-06-24 12:42:57.212][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:57.213][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:57.214][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:57.215][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:57.216][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:57.217][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:57.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:57.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:57.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:57.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:57.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:57.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:57.229][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[2024-06-24 12:42:57.230][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-06-24 12:42:57.233][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:57.234][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:57.235][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-06-24 12:42:57.305][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-06-24 12:42:57.382][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:57.385][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-06-24 12:42:57.389][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-06-24 12:42:57.392][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-06-24 12:42:57.394][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:57.396][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:57.397][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:57.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:57.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:57.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:57.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:57.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:57.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:57.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:57.411][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.412][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.414][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.419][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:57.420][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:57.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.421][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.422][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:57.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:57.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.426][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:57.427][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:57.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.429][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.430][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:57.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:57.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.433][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:57.434][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:57.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.436][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.437][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:57.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:57.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.452][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.453][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.455][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.456][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.459][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:57.460][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:57.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.462][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.463][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:57.464][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.465][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.467][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:57.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.470][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.471][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.473][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.477][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:57.478][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:57.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.480][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.481][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:57.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:57.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.484][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:57.485][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:57.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.487][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.488][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:57.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:57.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.492][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:57.493][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:57.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.494][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.495][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:57.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:57.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:57.532][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-06-24 12:42:57.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:57.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:57.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:57.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:57.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:57.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:57.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:57.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:57.562][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-06-24 12:42:57.563][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:57.565][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-06-24 12:42:57.566][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:57.567][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:57.568][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:57.569][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:57.570][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:57.571][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:57.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:57.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:57.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:57.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:57.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:57.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:57.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:57.585][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-06-24 12:42:57.588][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:57.589][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:57.590][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-06-24 12:42:57.660][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-06-24 12:42:57.729][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:57.732][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-06-24 12:42:57.736][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-06-24 12:42:57.739][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-06-24 12:42:57.742][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:57.743][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:57.744][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:57.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:57.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:57.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:57.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:57.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:57.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:57.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:57.758][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.759][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.760][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.765][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:57.766][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:57.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.767][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.768][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:57.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:57.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.772][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:57.773][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:57.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.774][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:57.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:57.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.779][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:57.780][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:57.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.781][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:57.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:57.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.786][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.787][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.788][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:57.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.793][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:57.794][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:57.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.796][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.797][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:57.809][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.812][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.813][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:57.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.819][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.820][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:57.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.825][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:57.826][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:57.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.828][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:57.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:57.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.833][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:57.834][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:57.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.835][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.836][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:57.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:57.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.840][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:57.840][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:57.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.842][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.843][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:57.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:57.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:57.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:57.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:57.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:57.881][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-06-24 12:42:57.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:57.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:57.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:57.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:57.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:57.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:57.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:57.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:57.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:57.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:57.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:57.902][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-06-24 12:42:57.903][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:57.905][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-06-24 12:42:57.906][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:57.907][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:57.915][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:57.917][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:57.918][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:57.919][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:57.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:57.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:57.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:57.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:57.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:57.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:57.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:57.934][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-06-24 12:42:57.937][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:57.938][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:57.940][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-06-24 12:42:58.016][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-06-24 12:42:58.088][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:58.091][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-06-24 12:42:58.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-06-24 12:42:58.098][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-06-24 12:42:58.100][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:58.101][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:58.102][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:58.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:58.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:58.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:58.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:58.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:58.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:58.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:58.116][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.117][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.119][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.124][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:58.125][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:58.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.126][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.127][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:58.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:58.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.131][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:58.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:58.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.133][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.135][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:58.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:58.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.138][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:58.139][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:58.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.141][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:58.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:58.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.147][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:58.148][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:58.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.149][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:58.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:58.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.155][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:58.156][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:58.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.157][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.158][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:58.159][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.161][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.162][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:58.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.165][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.166][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.168][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.180][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:58.185][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:58.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.187][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:58.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:58.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.192][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:58.193][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:58.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.195][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.196][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:58.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:58.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.199][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:58.200][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:58.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.202][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.203][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:58.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:58.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:58.243][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-06-24 12:42:58.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:58.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:58.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:58.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:58.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:58.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:58.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:58.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:58.265][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-06-24 12:42:58.266][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:58.268][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-06-24 12:42:58.269][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:58.270][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:58.271][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:58.272][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:58.273][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:58.273][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:58.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:58.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:58.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:58.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:58.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:58.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:58.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:58.295][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-06-24 12:42:58.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:58.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:58.302][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-06-24 12:42:58.375][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-06-24 12:42:58.448][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:58.451][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-06-24 12:42:58.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-06-24 12:42:58.459][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-06-24 12:42:58.460][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:58.462][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:58.463][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:58.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:58.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:58.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:58.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:58.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:58.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:58.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:58.478][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.479][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.481][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.486][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:58.488][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:58.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.489][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.491][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:58.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:58.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.494][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:58.495][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:58.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.497][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.498][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:58.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:58.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.502][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:58.503][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:58.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.504][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:58.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:58.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.509][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:58.510][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:58.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.511][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:58.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:58.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.516][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:58.517][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:58.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.518][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.520][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:58.520][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.522][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.523][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:58.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.527][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.528][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.529][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.534][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:58.535][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:58.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.536][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:58.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:58.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.541][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:58.542][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:58.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.544][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.545][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:58.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:58.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.559][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:58.561][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:58.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.562][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.563][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:58.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:58.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:58.604][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-06-24 12:42:58.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:58.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:58.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:58.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:58.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:58.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:58.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:58.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:58.627][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-06-24 12:42:58.628][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:58.630][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-06-24 12:42:58.632][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:58.633][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:58.634][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:58.636][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:58.637][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:58.637][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:58.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:58.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:58.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:58.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:58.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:58.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:58.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:58.651][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-06-24 12:42:58.654][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:58.655][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:58.656][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-06-24 12:42:58.731][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-06-24 12:42:58.805][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:58.807][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-06-24 12:42:58.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-06-24 12:42:58.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-06-24 12:42:58.826][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:58.827][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:58.828][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:58.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:58.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:58.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:58.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:58.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:58.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:58.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:58.842][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.843][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.844][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.849][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:58.850][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:58.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.851][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.852][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:58.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:58.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.856][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:58.857][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:58.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.858][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.859][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:58.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:58.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.863][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:58.864][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:58.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.865][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.866][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:58.867][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:58.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.869][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.870][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:58.870][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:58.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.872][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.873][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:58.874][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.876][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.877][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:58.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.880][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.881][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.882][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:58.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.887][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:58.888][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:58.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.889][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:58.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:58.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.894][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:58.895][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:58.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.896][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.897][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:58.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:58.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.900][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:58.901][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:58.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.903][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:58.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:58.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:58.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:58.946][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-06-24 12:42:58.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:58.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:58.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:58.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:58.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:58.959][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:58.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:58.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:58.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:58.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:58.967][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[2024-06-24 12:42:58.968][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-06-24 12:42:58.969][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:58.971][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-06-24 12:42:58.972][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:58.973][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:58.974][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:58.975][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:58.976][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:58.977][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:58.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:58.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:58.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:58.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:58.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:58.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:58.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:58.992][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-06-24 12:42:58.996][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:58.997][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:42:58.999][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-06-24 12:42:59.068][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-06-24 12:42:59.134][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:59.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-06-24 12:42:59.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-06-24 12:42:59.140][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-06-24 12:42:59.141][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:59.142][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:59.142][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:59.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:59.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:59.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:59.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:59.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:59.150][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:59.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:59.152][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.153][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.154][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.162][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:59.167][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:59.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.169][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.170][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:59.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:59.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.172][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:59.173][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:59.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.174][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.174][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:59.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:59.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.176][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:59.176][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:59.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.177][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.178][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:59.178][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:59.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.179][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.179][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:59.180][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:59.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.180][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.181][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:59.181][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.182][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.183][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:59.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.187][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.188][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.190][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.194][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:59.195][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:59.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.196][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:59.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:59.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.199][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:59.201][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:59.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.203][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.204][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:59.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:59.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.208][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:59.208][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:59.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.209][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:59.230][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-06-24 12:42:59.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:59.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:59.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:59.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:59.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:59.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:59.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:59.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:59.248][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-06-24 12:42:59.248][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:59.249][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-06-24 12:42:59.250][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:59.250][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:59.251][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:59.251][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:59.251][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:59.252][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:59.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:59.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:59.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:59.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:59.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:59.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:59.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:59.260][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-06-24 12:42:59.261][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:59.262][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:42:59.262][rule$waitAsNeeded] Wait 0.0389352 second(s).
biodb.TRACE[2024-06-24 12:42:59.303][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-06-24 12:42:59.375][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-06-24 12:42:59.436][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:59.437][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-06-24 12:42:59.439][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-06-24 12:42:59.442][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-06-24 12:42:59.444][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:59.445][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:59.447][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:59.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:59.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:59.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:59.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:59.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:59.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:59.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:59.462][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.463][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.464][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.469][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:59.470][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:59.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.471][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.473][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:59.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:59.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.477][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:59.478][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:59.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.480][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.481][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:59.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:59.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.486][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:59.487][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:59.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.490][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:59.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:59.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.505][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:59.507][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:59.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.510][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:59.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:59.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.512][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:59.513][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:59.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.513][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.514][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:59.514][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.515][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.515][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:59.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.517][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.517][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.518][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.520][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:59.521][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:59.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.521][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:59.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:59.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.523][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:59.524][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:59.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.524][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.525][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:59.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:59.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.526][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:59.527][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:59.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.527][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.528][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:59.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:59.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:59.543][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-06-24 12:42:59.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:59.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:59.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:59.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:59.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:59.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:59.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:59.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:59.561][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-06-24 12:42:59.561][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:59.562][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-06-24 12:42:59.563][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:59.563][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:59.564][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:59.564][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:59.565][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:59.565][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:59.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:59.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:59.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:59.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:59.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:59.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:59.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:59.575][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-06-24 12:42:59.578][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:59.578][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:42:59.579][rule$waitAsNeeded] Wait 0.0767441 second(s).
biodb.TRACE[2024-06-24 12:42:59.657][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-06-24 12:42:59.729][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-06-24 12:42:59.796][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:42:59.798][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-06-24 12:42:59.800][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-06-24 12:42:59.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-06-24 12:42:59.802][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:42:59.802][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:42:59.803][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:42:59.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:59.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:59.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:59.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:59.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:59.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:59.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:42:59.811][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.812][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.813][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.816][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:59.816][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:59.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.817][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.818][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:42:59.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:42:59.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.820][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:59.820][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:59.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.821][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.821][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:42:59.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:42:59.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.823][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:59.823][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:59.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.824][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:42:59.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:42:59.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.826][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:59.826][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:59.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.827][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:42:59.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:42:59.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.829][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:59.829][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:42:59.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.839][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.843][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:59.844][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.846][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.847][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:42:59.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.848][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.849][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.849][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:42:59.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.851][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:59.852][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:59.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.853][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:42:59.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:42:59.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.856][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:59.856][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:59.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.857][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.858][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:42:59.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:42:59.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.859][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:59.859][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:59.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.860][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.861][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:42:59.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:42:59.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:42:59.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:42:59.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:42:59.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:59.876][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-06-24 12:42:59.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:42:59.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:42:59.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:42:59.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:42:59.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:59.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:59.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:59.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:59.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:59.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:59.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:42:59.887][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-06-24 12:42:59.887][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:42:59.888][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-06-24 12:42:59.894][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:42:59.896][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:42:59.897][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:42:59.898][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:42:59.899][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:42:59.899][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:42:59.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:42:59.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:42:59.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:42:59.905][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:42:59.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:42:59.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:42:59.906][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[2024-06-24 12:42:59.907][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-06-24 12:42:59.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:42:59.909][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:42:59.910][rule$waitAsNeeded] Wait 0.088809 second(s).
biodb.TRACE[2024-06-24 12:43:00.150][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-06-24 12:43:00.228][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-06-24 12:43:00.297][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:00.300][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-06-24 12:43:00.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-06-24 12:43:00.307][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-06-24 12:43:00.309][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:43:00.310][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:00.311][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:43:00.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:00.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:00.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:00.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:00.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:00.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:00.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:00.327][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.328][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.330][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.335][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:00.336][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:00.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.337][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.338][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:00.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:00.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.342][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:00.343][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:00.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.345][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.346][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:00.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:00.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.351][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:00.352][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:00.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.353][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:00.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:00.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.358][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:00.359][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:00.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.361][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:00.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:00.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.365][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:00.366][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:00.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.368][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.369][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:00.370][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.371][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.372][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:00.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.376][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:00.377][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:00.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:00.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:00.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.396][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:00.398][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:00.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.399][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:00.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:00.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.405][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:00.406][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:00.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.407][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.408][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:00.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:00.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.412][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:00.413][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:00.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.414][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.416][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:00.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:00.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:00.457][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-06-24 12:43:00.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:00.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:00.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:00.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:00.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:00.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:00.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:00.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:00.481][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-06-24 12:43:00.482][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:43:00.484][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-06-24 12:43:00.485][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:43:00.486][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:43:00.487][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:00.488][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:00.489][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:43:00.490][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:43:00.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:00.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:00.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:00.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:00.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:00.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:00.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:00.513][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-06-24 12:43:00.516][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:00.517][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:00.518][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-06-24 12:43:00.595][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-06-24 12:43:00.665][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:00.668][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-06-24 12:43:00.672][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-06-24 12:43:00.674][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-06-24 12:43:00.676][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:43:00.677][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:00.679][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:43:00.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:00.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:00.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:00.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:00.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:00.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:00.690][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.TRACE[2024-06-24 12:43:00.692][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.694][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.695][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.700][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:00.701][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:00.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.703][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.704][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:00.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:00.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.707][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:00.708][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:00.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.710][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:00.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:00.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.714][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:00.715][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:00.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.717][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:00.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:00.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.721][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:00.722][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:00.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.723][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:00.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:00.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.728][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:00.728][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:00.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.730][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.731][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:00.732][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.733][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.734][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:00.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.738][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:00.738][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:00.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.740][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:00.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:00.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.744][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:00.745][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:00.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.747][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.748][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:00.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:00.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.752][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:00.753][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:00.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.754][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.766][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:00.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:00.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.771][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:00.772][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:00.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.774][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.775][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:00.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:00.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:00.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:00.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:00.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:00.814][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-06-24 12:43:00.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:00.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:00.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:00.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:00.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:00.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:00.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:00.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:00.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:00.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:00.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:00.836][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-06-24 12:43:00.837][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:43:00.838][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-06-24 12:43:00.839][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:43:00.841][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:43:00.842][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:00.843][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:00.844][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:43:00.844][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:43:00.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:00.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:00.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:00.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:00.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:00.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:00.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:00.859][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-06-24 12:43:00.862][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:00.864][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:00.865][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-06-24 12:43:00.939][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-06-24 12:43:01.011][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:01.013][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-06-24 12:43:01.028][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-06-24 12:43:01.032][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-06-24 12:43:01.033][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:43:01.035][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:01.036][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:43:01.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:01.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:01.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:01.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:01.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:01.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:01.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:01.050][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.051][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.052][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.057][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:01.058][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:01.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.059][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.061][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:01.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:01.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.064][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:01.065][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:01.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.068][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.069][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:01.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:01.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.073][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:01.074][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:01.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.075][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.076][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:01.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:01.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.080][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.081][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.082][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.087][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:01.088][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:01.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.089][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.090][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:01.091][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.093][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.094][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:01.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.097][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.098][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.100][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.104][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:01.105][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:01.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.107][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:01.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:01.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.111][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:01.112][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:01.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.114][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.115][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:01.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:01.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.118][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:01.119][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:01.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.120][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.121][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:01.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:01.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:01.168][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-06-24 12:43:01.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:01.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:01.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:01.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:01.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:01.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:01.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:01.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:01.189][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-06-24 12:43:01.190][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:43:01.192][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-06-24 12:43:01.193][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:43:01.194][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:43:01.195][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:01.196][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:01.196][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:43:01.197][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:43:01.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:01.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:01.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:01.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:01.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:01.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:01.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:01.211][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-06-24 12:43:01.214][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:01.215][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:01.216][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-06-24 12:43:01.290][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-06-24 12:43:01.362][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:01.364][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-06-24 12:43:01.368][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-06-24 12:43:01.370][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-06-24 12:43:01.372][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:43:01.373][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:01.374][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:43:01.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:01.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:01.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:01.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:01.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:01.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:01.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:01.398][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.400][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.401][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.406][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:01.407][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:01.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.408][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.409][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:01.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:01.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.413][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:01.414][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:01.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.416][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.418][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:01.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:01.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.422][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:01.422][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:01.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.424][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:01.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:01.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.430][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.431][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.432][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.433][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.439][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:01.440][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:01.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.442][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.443][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:01.444][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.446][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.447][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:01.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.450][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.451][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.453][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.457][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:01.458][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:01.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.460][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:01.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:01.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.464][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:01.465][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:01.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.467][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.468][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:01.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:01.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.471][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:01.472][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:01.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.474][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.475][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:01.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:01.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:01.522][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-06-24 12:43:01.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:01.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:01.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:01.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:01.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:01.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:01.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:01.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:01.544][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-06-24 12:43:01.545][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:43:01.547][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-06-24 12:43:01.548][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:43:01.549][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:43:01.550][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:01.551][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:01.552][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:43:01.552][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:43:01.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:01.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:01.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:01.562][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:01.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:01.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:01.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:01.566][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-06-24 12:43:01.569][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:01.570][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:01.571][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-06-24 12:43:01.649][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-06-24 12:43:01.717][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:01.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-06-24 12:43:01.724][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-06-24 12:43:01.727][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-06-24 12:43:01.728][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:43:01.729][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:01.731][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:43:01.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:01.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:01.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:01.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:01.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:01.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:01.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:01.744][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.745][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.747][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.763][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:01.764][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:01.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.766][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.767][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:01.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:01.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.771][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:01.772][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:01.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.774][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:01.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:01.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.779][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:01.780][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:01.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.782][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:01.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:01.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.787][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.788][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.789][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.790][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:01.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.794][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:01.795][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:01.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.797][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.798][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:01.800][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.802][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.803][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:01.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.807][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.808][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.809][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:01.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.814][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:01.815][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:01.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.816][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:01.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:01.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.822][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:01.823][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:01.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.825][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.826][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:01.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:01.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.830][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:01.830][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:01.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.832][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.833][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:01.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:01.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:01.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:01.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:01.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:01.884][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-06-24 12:43:01.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:01.917][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:01.920][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:01.922][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 12:43:01.923][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:01.924][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 12:43:01.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:01.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:01.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:01.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:01.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:01.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:01.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:01.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:01.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:01.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:01.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:01.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:01.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:01.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:01.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:01.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:01.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:01.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:01.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:01.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:01.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:01.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:01.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:01.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:01.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:01.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:01.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.202][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:02.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:02.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:02.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:02.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:02.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:02.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:02.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:02.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:02.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:02.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:02.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:02.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:02.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:02.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:02.478][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:02.482][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:02.483][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:02.485][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:43:02.559][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:43:02.630][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:02.632][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-06-24 12:43:02.637][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-06-24 12:43:02.642][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:02.645][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:02.647][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:02.649][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:43:02.731][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:43:02.803][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:02.806][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-06-24 12:43:02.810][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-06-24 12:43:02.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:02.824][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-06-24 12:43:02.825][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:43:02.826][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-06-24 12:43:02.827][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:43:02.828][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:43:02.829][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:02.830][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:02.831][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:43:02.832][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:43:02.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:02.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:02.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:02.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:02.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:02.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:02.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:02.860][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-06-24 12:43:02.863][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:02.864][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:02.865][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-06-24 12:43:02.934][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-06-24 12:43:03.008][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:03.010][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-06-24 12:43:03.015][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-06-24 12:43:03.018][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-06-24 12:43:03.020][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:43:03.021][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:03.022][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:43:03.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:03.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:03.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:03.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:03.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:03.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:03.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:03.037][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.038][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.040][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.045][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:03.046][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:03.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.048][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.050][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:03.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:03.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.054][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:03.055][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:03.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.056][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.058][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:03.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:03.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.061][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:03.062][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:03.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.064][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:03.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:03.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.069][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:03.070][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:03.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.072][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:03.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:03.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.076][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:03.077][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:03.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.079][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.080][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:03.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:03.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.084][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:03.085][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:03.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.086][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.087][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:03.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:03.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.091][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.093][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.097][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:03.098][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:03.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.107][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:03.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:03.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.118][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:03.119][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:03.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.120][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.121][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:03.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:03.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.126][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:03.127][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:03.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.128][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.129][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:03.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:03.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:03.168][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-06-24 12:43:03.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:03.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:03.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:03.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:03.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:03.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:03.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:03.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:03.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:03.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:03.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:03.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:03.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:03.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:03.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:03.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:03.226][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-06-24 12:43:03.228][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:43:03.231][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-06-24 12:43:03.233][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:43:03.235][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:43:03.236][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:03.237][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:03.237][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:43:03.238][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:43:03.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:03.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:03.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:03.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:03.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:03.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:03.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:03.252][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-06-24 12:43:03.255][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:03.256][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-06-24 12:43:03.257][rule$waitAsNeeded] Wait 0.22733 second(s).
biodb.TRACE[2024-06-24 12:43:03.636][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-06-24 12:43:03.708][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-06-24 12:43:03.778][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:03.780][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-06-24 12:43:03.785][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-06-24 12:43:03.788][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-06-24 12:43:03.790][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:43:03.791][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:03.792][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:43:03.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:03.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:03.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:03.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:03.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:03.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:03.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:03.807][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.808][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.810][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.814][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:03.815][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:03.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.817][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.818][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:03.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:03.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.822][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:03.823][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:03.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.824][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:03.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:03.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.829][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:03.830][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:03.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.832][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.833][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:03.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:03.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.836][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:03.837][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:03.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.838][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.839][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:03.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:03.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.843][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:03.844][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:03.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.845][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.846][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:03.847][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:03.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.849][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.850][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:03.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:03.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.865][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.866][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.868][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.872][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:03.873][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:03.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.875][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:03.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:03.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.879][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:03.880][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:03.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.882][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.883][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:03.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:03.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.886][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:03.887][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:03.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.889][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.890][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:03.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:03.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:03.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:03.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:03.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:03.926][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-06-24 12:43:03.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:03.956][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:03.967][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:03.969][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 12:43:03.971][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:03.972][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 12:43:03.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:03.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:03.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:03.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:03.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:03.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:03.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:03.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:03.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:03.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:03.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:03.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:03.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:03.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.346][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.TRACE[2024-06-24 12:43:04.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.527][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[2024-06-24 12:43:04.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.574][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.TRACE[2024-06-24 12:43:04.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.710][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:04.714][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:04.715][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-24 12:43:04.716][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:04.717][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-24 12:43:04.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.810][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[2024-06-24 12:43:04.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.906][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.TRACE[2024-06-24 12:43:04.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:04.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:04.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:04.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:04.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:04.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:04.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:04.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:04.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:04.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:04.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:04.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.034][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.096][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[2024-06-24 12:43:05.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.170][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.178][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.179][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[2024-06-24 12:43:05.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.205][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 12:43:05.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 12:43:05.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:05.217][biodb::testThat]
biodb.INFO [2024-06-24 12:43:05.218][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-24 12:43:05.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:05.220][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:05.223][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:05.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:05.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.253][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[2024-06-24 12:43:05.256][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:05.260][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:05.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-24 12:43:05.263][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:05.264][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-24 12:43:05.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.277][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.TRACE[2024-06-24 12:43:05.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.290][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:05.293][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:05.295][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-24 12:43:05.296][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:05.297][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-24 12:43:05.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.332][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[2024-06-24 12:43:05.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:05.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.343][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 12:43:05.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.355][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[2024-06-24 12:43:05.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.363][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.364][private$selectFields]
biodb.TRACE[2024-06-24 12:43:05.365][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:05.366][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:05.366][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.367][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.376][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.379][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.380][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.381][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.382][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.383][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.384][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.385][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.387][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.388][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:05.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.409][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-24 12:43:05.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.429][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.430][private$selectFields]
biodb.TRACE[2024-06-24 12:43:05.431][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:05.432][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:05.432][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.433][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.435][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.437][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.439][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.440][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.442][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.444][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.445][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.446][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.447][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.448][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.449][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.450][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:05.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.461][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 12:43:05.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.480][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.481][private$selectFields]
biodb.TRACE[2024-06-24 12:43:05.482][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:05.483][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:05.483][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.484][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.485][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.488][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.489][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.490][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.491][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.492][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.493][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:05.494][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.495][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.498][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.499][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:05.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:05.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.510][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-24 12:43:05.511][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 12:43:05.512][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 12:43:05.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:05.604][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:05.607][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:05.608][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:05.610][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:43:05.686][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:43:05.754][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:05.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-06-24 12:43:05.762][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-06-24 12:43:05.766][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:05.770][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:05.771][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:05.773][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:43:05.844][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:43:05.922][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:05.925][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-06-24 12:43:05.930][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-06-24 12:43:05.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.945][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.TRACE[2024-06-24 12:43:05.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.965][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:05.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:05.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:05.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:05.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:05.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:05.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:05.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:05.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:05.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:05.987][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.TRACE[2024-06-24 12:43:05.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:05.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.037][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 12:43:06.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.079][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.080][private$selectFields]
biodb.TRACE[2024-06-24 12:43:06.081][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:06.081][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:06.082][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.083][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.084][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.086][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.087][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.089][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.091][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.092][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.093][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.096][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.097][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.098][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:06.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.109][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-24 12:43:06.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.162][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.163][private$selectFields]
biodb.TRACE[2024-06-24 12:43:06.164][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:06.165][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:06.166][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.167][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.168][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.169][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.170][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.171][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.173][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.174][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.185][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.186][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.188][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.189][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.190][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:06.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.202][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 12:43:06.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.212][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.TRACE[2024-06-24 12:43:06.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.220][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.221][private$selectFields]
biodb.TRACE[2024-06-24 12:43:06.222][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:06.223][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:06.223][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.224][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.225][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.227][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.227][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.228][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.230][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.231][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.232][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.236][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.236][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:06.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.248][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-24 12:43:06.248][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 12:43:06.249][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 12:43:06.259][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 12:43:06.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 12:43:06.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:06.266][biodb::testThat]
biodb.INFO [2024-06-24 12:43:06.268][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-24 12:43:06.268][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:06.269][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:06.273][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:06.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:06.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:06.306][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:06.310][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:06.311][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-24 12:43:06.319][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:06.320][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-24 12:43:06.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.332][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[2024-06-24 12:43:06.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.343][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:06.346][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:06.348][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-24 12:43:06.349][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:06.350][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-24 12:43:06.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.362][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.TRACE[2024-06-24 12:43:06.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.382][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[2024-06-24 12:43:06.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.393][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 12:43:06.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.411][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.412][private$selectFields]
biodb.TRACE[2024-06-24 12:43:06.413][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:06.414][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:06.414][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.415][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.416][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.418][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.418][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.419][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.421][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.422][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.422][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.423][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.424][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.426][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.426][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:06.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.437][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-24 12:43:06.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.456][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.457][private$selectFields]
biodb.TRACE[2024-06-24 12:43:06.457][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:06.458][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:06.459][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.460][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.461][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.462][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.463][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.464][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.465][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.465][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.466][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.467][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.468][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.469][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.470][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.471][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:06.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.482][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 12:43:06.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.492][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.TRACE[2024-06-24 12:43:06.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.500][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.501][private$selectFields]
biodb.TRACE[2024-06-24 12:43:06.502][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:06.503][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:06.503][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.505][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.507][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.507][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.510][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.511][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.511][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.515][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.515][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:06.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.526][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-24 12:43:06.527][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 12:43:06.528][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 12:43:06.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:06.566][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:06.570][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:06.571][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-24 12:43:06.572][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:06.574][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-24 12:43:06.577][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:06.580][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:06.581][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-24 12:43:06.583][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:06.584][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-24 12:43:06.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:06.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.657][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 12:43:06.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.677][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.678][private$selectFields]
biodb.TRACE[2024-06-24 12:43:06.679][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:06.680][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:06.681][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.681][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.682][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.684][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.686][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.687][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.688][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.689][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.690][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.690][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.692][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.693][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:06.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.704][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-24 12:43:06.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.723][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.724][private$selectFields]
biodb.TRACE[2024-06-24 12:43:06.725][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:06.725][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:06.726][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.727][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.728][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.730][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.730][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.731][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.733][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.734][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.734][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.735][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.736][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.737][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.738][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:06.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.750][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 12:43:06.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.770][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.771][private$selectFields]
biodb.TRACE[2024-06-24 12:43:06.772][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:06.773][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:06.773][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.777][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.778][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.778][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.780][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.781][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.782][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.782][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.783][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.785][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.786][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:06.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.797][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-24 12:43:06.797][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 12:43:06.798][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 12:43:06.807][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 12:43:06.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 12:43:06.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:06.815][biodb::testThat]
biodb.INFO [2024-06-24 12:43:06.816][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-24 12:43:06.817][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:06.818][biodb::testThat]
biodb.TRACE[2024-06-24 12:43:06.821][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-24 12:43:06.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-24 12:43:06.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:06.859][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:06.862][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:06.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-24 12:43:06.865][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:06.867][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-24 12:43:06.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.881][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[2024-06-24 12:43:06.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.894][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:06.897][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:06.899][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-24 12:43:06.900][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:06.901][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-24 12:43:06.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.915][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.TRACE[2024-06-24 12:43:06.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.936][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.TRACE[2024-06-24 12:43:06.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:06.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:06.947][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 12:43:06.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:06.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:06.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:06.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:06.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:06.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:06.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:06.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.967][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.967][private$selectFields]
biodb.TRACE[2024-06-24 12:43:06.968][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:06.969][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:06.970][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.971][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.972][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.980][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.981][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.982][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.983][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.984][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.985][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:06.986][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.987][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.988][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.989][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:06.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:06.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:06.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:06.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.000][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-24 12:43:07.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.007][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:07.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.018][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.018][private$selectFields]
biodb.TRACE[2024-06-24 12:43:07.019][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:07.020][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:07.021][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.021][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.022][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.024][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.024][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.025][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.027][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.028][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.028][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.029][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.030][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.031][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.032][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:07.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.043][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 12:43:07.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:07.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.061][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.062][private$selectFields]
biodb.TRACE[2024-06-24 12:43:07.062][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:07.063][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:07.064][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.065][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.066][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.067][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.068][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.069][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.070][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.071][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.072][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.073][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.074][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.075][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.076][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:07.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.087][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-24 12:43:07.088][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 12:43:07.089][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 12:43:07.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:07.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:07.141][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:07.144][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:07.146][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-24 12:43:07.147][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:07.148][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-24 12:43:07.151][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:07.154][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:07.156][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-24 12:43:07.157][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:07.158][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-24 12:43:07.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:07.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:07.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:07.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:07.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.212][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.TRACE[2024-06-24 12:43:07.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:07.223][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-24 12:43:07.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.234][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[2024-06-24 12:43:07.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.242][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.243][private$selectFields]
biodb.TRACE[2024-06-24 12:43:07.244][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:07.244][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:07.245][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.246][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.247][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.248][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.249][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.250][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.251][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.252][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.253][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.254][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.255][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.256][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.257][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:07.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.268][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-24 12:43:07.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:07.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.286][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.287][private$selectFields]
biodb.TRACE[2024-06-24 12:43:07.287][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:07.288][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:07.289][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.297][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.298][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.299][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.300][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.302][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.303][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.304][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.306][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.307][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.308][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:07.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.318][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-24 12:43:07.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:07.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.336][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.337][private$selectFields]
biodb.TRACE[2024-06-24 12:43:07.338][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-24 12:43:07.339][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-24 12:43:07.339][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.340][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.343][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.344][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.344][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.347][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.348][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.349][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-24 12:43:07.350][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.350][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.352][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.353][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-24 12:43:07.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.364][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-24 12:43:07.365][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-24 12:43:07.365][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-24 12:43:07.384][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-24 12:43:07.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-24 12:43:07.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:07.392][biodb::testThat]
biodb.INFO [2024-06-24 12:43:07.393][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-24 12:43:07.394][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:07.394][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:07.396][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-24 12:43:07.397][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:43:07.398][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-24 12:43:07.400][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:43:07.401][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:43:07.402][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:07.402][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:07.403][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:43:07.404][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:43:07.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:07.417][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-06-24 12:43:07.420][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:07.421][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:07.423][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-06-24 12:43:07.551][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-06-24 12:43:07.626][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:07.629][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-06-24 12:43:07.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-06-24 12:43:07.638][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-06-24 12:43:07.640][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:43:07.642][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:07.643][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:43:07.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:07.658][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:07.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:07.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.660][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:07.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:07.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.665][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:07.666][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:07.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.668][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.669][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:07.670][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:07.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.671][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.673][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:07.674][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:07.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.675][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.676][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:07.677][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:07.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.679][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.680][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:07.681][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:07.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.682][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.683][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:07.684][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:07.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.686][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.687][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.688][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:07.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.689][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.691][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:07.691][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:07.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.693][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.694][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:07.696][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:07.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.697][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.699][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:07.699][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:07.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.701][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:07.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:07.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:07.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:07.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:07.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:07.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:07.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:07.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:07.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:07.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:07.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:07.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:07.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:07.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:07.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:07.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:07.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:07.738][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-06-24 12:43:07.739][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-24 12:43:07.749][biodb::testThat]
biodb.INFO [2024-06-24 12:43:07.751][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-24 12:43:07.752][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:07.753][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:07.765][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-06-24 12:43:07.767][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-06-24 12:43:07.768][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-06-24 12:43:07.769][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-06-24 12:43:07.770][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2024-06-24 12:43:07.772][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2024-06-24 12:43:07.773][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:07.774][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:07.775][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:43:07.776][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:43:07.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:07.790][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-06-24 12:43:07.793][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:07.794][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:07.795][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-06-24 12:43:07.869][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-06-24 12:43:07.940][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:07.942][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-06-24 12:43:07.946][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-06-24 12:43:07.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:07.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:07.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:07.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:07.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:07.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:07.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:07.960][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-06-24 12:43:07.964][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:07.966][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:07.967][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-06-24 12:43:08.039][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-06-24 12:43:08.114][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:08.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-06-24 12:43:08.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-06-24 12:43:08.124][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-06-24 12:43:08.126][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:43:08.143][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-06-24 12:43:08.145][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-06-24 12:43:08.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:08.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:08.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:08.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:08.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:08.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:08.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:08.160][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.161][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.162][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.167][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:08.168][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:08.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.169][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.171][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:08.172][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:08.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.173][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.174][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:08.175][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:08.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.177][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.178][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:08.179][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:08.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.180][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.181][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:08.182][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:08.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.184][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.185][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:08.186][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:08.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.187][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.188][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.189][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.191][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.192][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:08.193][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:08.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.194][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.195][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:08.196][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:08.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.198][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.199][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:08.200][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:08.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.201][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:08.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:08.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:08.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:08.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:08.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:08.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:08.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:08.237][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.238][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.239][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.244][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:08.245][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:08.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.246][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.247][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:08.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:08.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.251][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:08.251][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:08.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.253][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.254][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:08.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:08.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.258][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:08.259][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:08.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.260][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:08.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:08.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.265][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:08.265][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:08.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.267][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:08.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:08.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.271][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:08.272][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:08.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.273][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.274][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:08.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:08.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.278][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:08.279][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:08.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.280][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.281][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:08.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:08.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.285][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.286][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.287][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.292][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:08.293][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:08.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.294][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:08.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:08.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.299][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:08.299][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:08.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.301][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.302][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:08.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:08.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.305][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:08.306][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:08.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.307][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.309][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:08.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:08.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:08.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:08.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:08.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:08.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:08.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:08.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:08.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:08.347][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.348][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.349][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.354][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:08.355][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:08.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.356][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.357][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:08.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:08.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.361][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:08.361][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:08.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.363][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:08.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:08.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.369][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:08.370][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:08.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.371][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:08.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:08.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.376][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:08.377][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:08.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:08.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:08.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.383][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:08.384][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:08.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.385][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.386][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:08.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:08.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.390][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:08.390][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:08.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.392][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.393][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:08.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:08.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.396][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.397][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.399][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.403][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:08.404][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:08.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.405][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:08.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:08.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.410][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:08.411][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:08.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.412][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.413][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:08.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:08.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.416][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:08.417][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:08.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.419][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.420][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:08.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:08.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:08.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:08.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:08.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:08.482][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-06-24 12:43:08.483][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-24 12:43:08.484][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-06-24 12:43:08.498][biodb::testThat]
biodb.INFO [2024-06-24 12:43:08.500][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-24 12:43:08.501][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:08.501][biodb::testThat]
biodb.INFO [2024-06-24 12:43:08.528][biodb::testThat]
biodb.INFO [2024-06-24 12:43:08.529][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-24 12:43:08.530][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:08.531][biodb::testThat]
biodb.INFO [2024-06-24 12:43:08.540][biodb::testThat]
biodb.INFO [2024-06-24 12:43:08.541][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-24 12:43:08.542][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:08.543][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:08.545][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:08.550][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:08.551][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:08.554][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:43:08.730][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:43:08.887][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:08.890][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-06-24 12:43:08.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-06-24 12:43:08.908][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:08.909][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:08.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.911][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:08.912][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.913][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:08.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:08.914][ef$get] fields variable is a list.
biodb.INFO [2024-06-24 12:43:08.916][biodb::testThat]
biodb.INFO [2024-06-24 12:43:08.917][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-24 12:43:08.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:08.918][biodb::testThat]
biodb.ERROR[2024-06-24 12:43:08.933][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-24 12:43:08.951][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-24 12:43:08.965][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 12:43:08.967][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 12:43:08.968][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 12:43:08.968][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 12:43:08.969][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:08.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:08.971][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:08.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:08.972][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:08.973][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.INFO [2024-06-24 12:43:08.983][biodb::testContext]
biodb.INFO [2024-06-24 12:43:08.985][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:08.986][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-06-24 12:43:08.986][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:08.987][biodb::testContext]
biodb.INFO [2024-06-24 12:43:08.989][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:08.991][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:08.996][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:08.997][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 12:43:08.998][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 12:43:08.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:08.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.001][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 12:43:09.002][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 12:43:09.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.005][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 12:43:09.005][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 12:43:09.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.008][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 12:43:09.009][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 12:43:09.010][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 12:43:09.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.013][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 12:43:09.014][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 12:43:09.014][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 12:43:09.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.017][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 12:43:09.018][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 12:43:09.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.021][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 12:43:09.022][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 12:43:09.023][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 12:43:09.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.026][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 12:43:09.026][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 12:43:09.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.029][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 12:43:09.030][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 12:43:09.031][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 12:43:09.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.034][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:09.035][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 12:43:09.035][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 12:43:09.036][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 12:43:09.037][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 12:43:09.038][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 12:43:09.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.041][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 12:43:09.041][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 12:43:09.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.044][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 12:43:09.045][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 12:43:09.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.048][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 12:43:09.049][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 12:43:09.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.051][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 12:43:09.052][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 12:43:09.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.055][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 12:43:09.056][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 12:43:09.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.059][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:09.060][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 12:43:09.076][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 12:43:09.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.080][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 12:43:09.081][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 12:43:09.082][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 12:43:09.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.085][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 12:43:09.087][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.088][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 12:43:09.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:09.091][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.092][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.092][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.093][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.094][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:09.095][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:09.096][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.097][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 12:43:09.097][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:09.098][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.099][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.100][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:09.100][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:09.100][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:09.100][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:09.100][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:09.101][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:09.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:09.102][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:09.103][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:09.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:09.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:09.106][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.106][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.107][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:09.119][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:09.120][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.121][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.122][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 12:43:09.124][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.125][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:09.126][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.127][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:09.128][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.128][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.129][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.130][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.131][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:09.132][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:09.133][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.134][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 12:43:09.135][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:09.135][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.136][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.137][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:09.137][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:09.137][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:09.137][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:09.137][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:09.138][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:09.139][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:09.139][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:09.140][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:09.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:09.141][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:09.142][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.143][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.144][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:09.144][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:09.145][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.146][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.147][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 12:43:09.149][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.150][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 12:43:09.150][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.151][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:09.152][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.153][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.153][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.154][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.155][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:09.156][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:09.157][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.158][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 12:43:09.159][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:09.160][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.161][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.162][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.163][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:09.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:09.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:09.166][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:09.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:09.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:09.168][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.169][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.169][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:09.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:09.171][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.172][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.173][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 12:43:09.175][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.176][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:09.177][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.178][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:09.179][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.179][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.180][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.181][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.182][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:09.182][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:09.183][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.184][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 12:43:09.185][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:09.186][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.186][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.187][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.188][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:09.189][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:09.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:09.190][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:09.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:09.192][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:09.193][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.193][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.194][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:09.195][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:09.196][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.197][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:09.198][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:09.198][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.218][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[2024-06-24 12:43:09.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.222][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[2024-06-24 12:43:09.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.229][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[2024-06-24 12:43:09.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.233][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[2024-06-24 12:43:09.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.240][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.DEBUG[2024-06-24 12:43:09.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.253][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[2024-06-24 12:43:09.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.257][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[2024-06-24 12:43:09.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.262][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 12:43:09.263][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 12:43:09.264][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 12:43:09.265][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 12:43:09.267][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:43:09.268][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:43:09.269][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:09.270][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:09.271][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 12:43:09.273][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:43:09.274][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:09.275][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 12:43:09.276][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:09.277][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:09.278][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 12:43:09.280][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:09.281][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 12:43:09.282][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 12:43:09.283][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:43:09.284][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 12:43:09.285][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 12:43:09.287][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 12:43:09.288][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 12:43:09.289][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 12:43:09.290][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 12:43:09.291][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 12:43:09.292][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 12:43:09.293][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 12:43:09.295][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 12:43:09.296][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 12:43:09.297][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 12:43:09.298][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 12:43:09.299][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 12:43:09.300][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 12:43:09.301][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 12:43:09.303][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 12:43:09.304][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 12:43:09.305][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 12:43:09.306][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 12:43:09.307][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 12:43:09.308][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 12:43:09.309][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 12:43:09.311][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 12:43:09.312][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 12:43:09.313][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 12:43:09.314][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 12:43:09.315][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 12:43:09.316][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 12:43:09.318][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 12:43:09.319][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 12:43:09.320][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 12:43:09.321][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 12:43:09.322][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 12:43:09.323][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 12:43:09.324][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 12:43:09.325][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 12:43:09.327][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 12:43:09.328][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 12:43:09.329][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 12:43:09.330][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 12:43:09.331][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 12:43:09.332][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 12:43:09.333][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 12:43:09.335][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 12:43:09.336][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 12:43:09.337][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 12:43:09.338][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:43:09.339][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:43:09.340][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 12:43:09.342][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 12:43:09.343][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 12:43:09.344][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 12:43:09.345][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 12:43:09.346][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 12:43:09.347][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 12:43:09.348][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 12:43:09.349][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 12:43:09.351][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 12:43:09.352][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 12:43:09.353][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 12:43:09.354][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 12:43:09.355][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 12:43:09.356][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 12:43:09.358][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 12:43:09.359][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:09.360][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:09.361][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.362][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.383][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.DEBUG[2024-06-24 12:43:09.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.405][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[2024-06-24 12:43:09.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.410][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[2024-06-24 12:43:09.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.415][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[2024-06-24 12:43:09.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.444][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.DEBUG[2024-06-24 12:43:09.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:09.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.455][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:09.456][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 12:43:09.458][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.459][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.460][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:09.461][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.462][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.463][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.464][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 12:43:09.464][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 12:43:09.465][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:09.466][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.467][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 12:43:09.468][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 12:43:09.469][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:09.470][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:09.470][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:09.470][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:09.471][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 12:43:09.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:09.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:09.473][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:09.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:09.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:09.475][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:09.476][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:09.476][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 12:43:09.477][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:09.478][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:09.478][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:09.479][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 12:43:09.479][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 12:43:09.480][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:43:09.482][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:09.483][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 12:43:09.485][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:43:09.486][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:43:09.487][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:43:09.490][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 12:43:09.491][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 12:43:09.492][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 12:43:09.494][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 12:43:09.495][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:09.496][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:09.497][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 12:43:09.498][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 12:43:09.499][biodb::testThat]
biodb.INFO [2024-06-24 12:43:09.500][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-06-24 12:43:09.501][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:09.502][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:09.506][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 12:43:09.510][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:09.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-24 12:43:09.512][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:09.514][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-24 12:43:09.518][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:09.523][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:09.525][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-24 12:43:09.526][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:09.528][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-24 12:43:09.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:09.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.541][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[2024-06-24 12:43:09.543][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:09.547][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:09.548][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-24 12:43:09.549][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:09.551][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-24 12:43:09.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:09.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:09.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.594][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:09.598][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:09.599][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-24 12:43:09.600][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:09.601][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-24 12:43:09.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:09.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.614][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:09.618][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:09.619][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-24 12:43:09.620][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:09.621][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-24 12:43:09.623][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:09.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:09.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.647][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:09.651][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:09.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-24 12:43:09.653][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:09.655][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-24 12:43:09.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:09.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.668][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:09.671][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:09.673][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-24 12:43:09.674][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:09.675][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-24 12:43:09.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:09.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.688][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[2024-06-24 12:43:09.690][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:09.693][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:09.695][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-06-24 12:43:09.696][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:09.698][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-06-24 12:43:09.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:09.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 12:43:09.717][biodb::testThat]
biodb.INFO [2024-06-24 12:43:09.718][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-06-24 12:43:09.719][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:09.719][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:09.723][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:09.727][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:09.728][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:09.738][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:43:09.857][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:43:09.927][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:09.930][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-06-24 12:43:09.935][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-06-24 12:43:09.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:09.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:09.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:09.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:09.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:09.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:09.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:09.953][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:09.957][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:09.958][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:09.959][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:43:10.033][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:43:10.106][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:10.109][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-06-24 12:43:10.113][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-06-24 12:43:10.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:10.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 12:43:10.132][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 12:43:10.134][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 12:43:10.135][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 12:43:10.135][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 12:43:10.136][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.138][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.139][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 12:43:10.144][biodb::testContext]
biodb.INFO [2024-06-24 12:43:10.145][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:10.146][biodb::testContext] Test context - Test web services
biodb.INFO [2024-06-24 12:43:10.147][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:10.147][biodb::testContext]
biodb.INFO [2024-06-24 12:43:10.150][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:10.151][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:10.157][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:10.158][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 12:43:10.159][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.162][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 12:43:10.163][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.166][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 12:43:10.167][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.170][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 12:43:10.171][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 12:43:10.172][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 12:43:10.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.174][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[2024-06-24 12:43:10.175][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 12:43:10.176][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 12:43:10.177][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.180][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 12:43:10.180][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 12:43:10.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.183][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 12:43:10.184][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 12:43:10.185][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 12:43:10.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.188][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 12:43:10.189][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.192][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 12:43:10.193][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 12:43:10.194][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.197][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:10.198][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 12:43:10.198][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 12:43:10.199][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 12:43:10.200][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 12:43:10.201][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 12:43:10.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.204][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 12:43:10.205][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 12:43:10.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.208][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 12:43:10.208][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 12:43:10.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.211][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 12:43:10.212][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 12:43:10.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.215][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 12:43:10.216][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 12:43:10.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.218][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[2024-06-24 12:43:10.219][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 12:43:10.220][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 12:43:10.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.224][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:10.225][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 12:43:10.241][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 12:43:10.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.244][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[2024-06-24 12:43:10.245][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 12:43:10.246][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 12:43:10.247][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 12:43:10.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.250][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 12:43:10.252][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.253][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 12:43:10.254][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.255][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:10.256][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.257][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.258][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.259][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.260][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:10.261][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:10.261][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.262][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 12:43:10.263][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:10.264][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.265][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.266][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:10.266][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:10.266][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:10.266][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:10.266][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:10.267][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:10.268][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:10.269][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:10.270][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:10.271][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:10.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:10.273][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.274][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.275][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:10.275][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:10.276][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.277][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.278][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 12:43:10.280][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.281][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:10.282][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.283][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:10.283][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.284][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.285][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.286][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.287][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:10.288][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:10.289][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.290][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 12:43:10.291][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:10.291][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.292][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.293][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:10.293][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:10.293][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:10.293][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:10.293][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:10.294][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:10.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:10.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:10.297][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:10.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:10.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:10.300][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.302][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.303][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:10.304][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:10.304][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.305][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.306][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 12:43:10.308][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.309][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 12:43:10.310][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.311][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:10.312][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.313][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.314][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.315][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.316][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:10.317][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:10.318][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.319][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 12:43:10.319][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:10.320][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.321][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.322][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.323][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:10.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:10.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:10.326][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:10.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:10.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:10.328][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.329][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.331][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:10.332][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:10.333][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.335][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.336][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 12:43:10.337][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.338][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:10.339][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.340][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:10.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.342][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.343][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.343][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.344][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:10.345][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:10.346][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.347][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 12:43:10.348][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:10.348][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.349][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.350][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.351][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:10.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:10.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:10.353][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:10.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:10.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:10.356][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.356][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.357][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:10.358][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:10.359][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.360][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:10.361][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:10.362][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.362][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[2024-06-24 12:43:10.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.389][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.DEBUG[2024-06-24 12:43:10.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.392][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[2024-06-24 12:43:10.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.410][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[2024-06-24 12:43:10.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.435][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[2024-06-24 12:43:10.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.439][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 12:43:10.440][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 12:43:10.442][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 12:43:10.443][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 12:43:10.444][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:43:10.445][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:43:10.446][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:10.448][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:10.449][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 12:43:10.450][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:43:10.451][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:10.452][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 12:43:10.454][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:10.455][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:10.456][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 12:43:10.457][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:10.458][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 12:43:10.459][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 12:43:10.461][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:43:10.462][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 12:43:10.463][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 12:43:10.464][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 12:43:10.466][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 12:43:10.467][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 12:43:10.468][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 12:43:10.469][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 12:43:10.470][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 12:43:10.472][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 12:43:10.473][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 12:43:10.474][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 12:43:10.475][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 12:43:10.477][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 12:43:10.478][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 12:43:10.479][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 12:43:10.481][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 12:43:10.482][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 12:43:10.483][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 12:43:10.484][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 12:43:10.486][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 12:43:10.487][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 12:43:10.488][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 12:43:10.489][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 12:43:10.491][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 12:43:10.492][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 12:43:10.493][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 12:43:10.494][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 12:43:10.496][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 12:43:10.497][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 12:43:10.498][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 12:43:10.499][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 12:43:10.501][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 12:43:10.502][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 12:43:10.503][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 12:43:10.504][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 12:43:10.505][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 12:43:10.507][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 12:43:10.508][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 12:43:10.509][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 12:43:10.511][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 12:43:10.512][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 12:43:10.513][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 12:43:10.514][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 12:43:10.516][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 12:43:10.517][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 12:43:10.518][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 12:43:10.519][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 12:43:10.520][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:43:10.521][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:43:10.523][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 12:43:10.525][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 12:43:10.526][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 12:43:10.528][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 12:43:10.529][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 12:43:10.530][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 12:43:10.531][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 12:43:10.532][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 12:43:10.534][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 12:43:10.535][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 12:43:10.536][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 12:43:10.537][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 12:43:10.538][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 12:43:10.539][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 12:43:10.541][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 12:43:10.542][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 12:43:10.544][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:10.545][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:10.545][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.547][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.552][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.DEBUG[2024-06-24 12:43:10.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.587][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[2024-06-24 12:43:10.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.611][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[2024-06-24 12:43:10.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.616][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[2024-06-24 12:43:10.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.626][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[2024-06-24 12:43:10.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.630][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[2024-06-24 12:43:10.632][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:10.634][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 12:43:10.636][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.637][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.638][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.639][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:10.639][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.640][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.641][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.642][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 12:43:10.643][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 12:43:10.643][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:10.644][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.645][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 12:43:10.646][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 12:43:10.647][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 12:43:10.648][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.649][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:10.649][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:10.649][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:10.649][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 12:43:10.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:10.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:10.652][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:10.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:10.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:10.654][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:10.655][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:10.655][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 12:43:10.656][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:10.656][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:10.657][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.658][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 12:43:10.658][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 12:43:10.659][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:43:10.660][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:10.662][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 12:43:10.663][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:43:10.664][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:43:10.666][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:43:10.669][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 12:43:10.670][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 12:43:10.671][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 12:43:10.672][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 12:43:10.674][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:10.674][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:10.676][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 12:43:10.676][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 12:43:10.678][biodb::testThat]
biodb.INFO [2024-06-24 12:43:10.679][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-06-24 12:43:10.687][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:10.688][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:10.691][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 12:43:10.695][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:10.697][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-24 12:43:10.698][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:10.699][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-24 12:43:10.703][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:10.706][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:10.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:10.709][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-24 12:43:10.781][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-24 12:43:10.852][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:10.854][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-06-24 12:43:10.859][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-06-24 12:43:10.869][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 12:43:10.871][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 12:43:10.872][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 12:43:10.873][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 12:43:10.873][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:10.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:10.875][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:10.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:10.877][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-24 12:43:10.882][biodb::testContext]
biodb.INFO [2024-06-24 12:43:10.883][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:10.884][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-06-24 12:43:10.885][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-24 12:43:10.885][biodb::testContext]
biodb.INFO [2024-06-24 12:43:10.888][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:10.890][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:10.895][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:10.896][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-24 12:43:10.897][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.901][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-24 12:43:10.901][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.905][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-24 12:43:10.905][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.908][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-24 12:43:10.909][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-24 12:43:10.910][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-24 12:43:10.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.913][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-24 12:43:10.914][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-24 12:43:10.915][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.918][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-24 12:43:10.919][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-24 12:43:10.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.922][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-24 12:43:10.923][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-24 12:43:10.924][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-24 12:43:10.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.926][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.DEBUG[2024-06-24 12:43:10.927][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-24 12:43:10.928][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.931][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-24 12:43:10.932][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-24 12:43:10.933][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-24 12:43:10.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.936][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:10.937][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-24 12:43:10.937][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-24 12:43:10.938][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-24 12:43:10.939][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-24 12:43:10.940][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-24 12:43:10.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.943][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-24 12:43:10.944][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-24 12:43:10.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.947][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-24 12:43:10.948][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-24 12:43:10.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.952][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-24 12:43:10.953][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-24 12:43:10.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.956][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-24 12:43:10.956][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-24 12:43:10.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.960][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-24 12:43:10.960][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-24 12:43:10.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.963][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-24 12:43:10.965][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-24 12:43:10.984][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-24 12:43:10.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:10.988][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-24 12:43:10.989][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-24 12:43:10.990][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-24 12:43:10.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:10.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:10.992][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[2024-06-24 12:43:10.993][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-24 12:43:10.995][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:10.996][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-24 12:43:10.997][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.998][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:10.999][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:10.999][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.001][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.002][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.003][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:11.003][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:11.004][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.005][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-24 12:43:11.006][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:11.007][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.007][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.008][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:11.008][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:11.008][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:11.008][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:11.008][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:11.009][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:11.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:11.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:11.011][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:11.012][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:11.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:11.014][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.014][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.015][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:11.016][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:11.017][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.017][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.018][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-24 12:43:11.020][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.021][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:11.022][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.023][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:11.024][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.024][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.025][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.026][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.027][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:11.028][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:11.029][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.029][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-24 12:43:11.030][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:11.031][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.032][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.033][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:11.033][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:11.033][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:11.033][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-24 12:43:11.033][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-24 12:43:11.034][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:11.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:11.035][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:11.036][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:11.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:11.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:11.038][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.039][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.040][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:11.041][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:11.041][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.042][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.043][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-24 12:43:11.045][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.046][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-24 12:43:11.046][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.047][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:11.048][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.049][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.050][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.050][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.051][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-24 12:43:11.052][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:11.053][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.054][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-24 12:43:11.054][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:11.055][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.056][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.057][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.058][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:11.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:11.059][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:11.060][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:11.061][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:11.061][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:11.062][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.063][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.064][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:11.064][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:11.065][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.066][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.067][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-24 12:43:11.068][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.069][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-24 12:43:11.070][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.071][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:11.072][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.072][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.073][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.074][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.075][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-24 12:43:11.076][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:11.076][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.077][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-24 12:43:11.078][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:11.080][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.081][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.082][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.083][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-24 12:43:11.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:11.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:11.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:11.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:11.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:11.088][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.088][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.089][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:11.090][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:11.091][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.091][self$setPropertyValue]
biodb.DEBUG[2024-06-24 12:43:11.093][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:11.093][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.169][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[2024-06-24 12:43:11.170][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-24 12:43:11.172][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-24 12:43:11.173][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-24 12:43:11.174][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-24 12:43:11.175][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:43:11.177][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-24 12:43:11.178][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:11.179][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:11.180][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-24 12:43:11.181][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-24 12:43:11.183][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:11.184][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-24 12:43:11.185][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-24 12:43:11.186][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-24 12:43:11.187][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-24 12:43:11.188][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-24 12:43:11.190][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-24 12:43:11.191][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-24 12:43:11.192][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:43:11.194][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-24 12:43:11.195][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-24 12:43:11.196][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-24 12:43:11.198][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-24 12:43:11.199][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-24 12:43:11.201][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-24 12:43:11.203][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-24 12:43:11.204][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-24 12:43:11.206][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-24 12:43:11.207][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-24 12:43:11.209][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-24 12:43:11.210][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-24 12:43:11.212][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-24 12:43:11.214][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-24 12:43:11.216][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-24 12:43:11.217][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-24 12:43:11.218][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-24 12:43:11.219][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-24 12:43:11.220][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-24 12:43:11.221][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-24 12:43:11.223][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-24 12:43:11.224][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-24 12:43:11.225][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-24 12:43:11.226][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-24 12:43:11.227][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-24 12:43:11.228][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-24 12:43:11.229][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-24 12:43:11.231][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-24 12:43:11.232][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-24 12:43:11.233][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-24 12:43:11.234][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-24 12:43:11.235][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-24 12:43:11.236][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-24 12:43:11.237][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-24 12:43:11.239][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-24 12:43:11.240][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-24 12:43:11.241][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-24 12:43:11.242][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-24 12:43:11.243][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-24 12:43:11.244][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-24 12:43:11.246][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-24 12:43:11.247][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-24 12:43:11.248][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-24 12:43:11.249][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-24 12:43:11.250][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-24 12:43:11.252][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-24 12:43:11.253][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-24 12:43:11.254][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:43:11.256][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:43:11.257][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-24 12:43:11.258][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-24 12:43:11.259][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-24 12:43:11.260][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-24 12:43:11.262][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-24 12:43:11.263][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-24 12:43:11.264][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-24 12:43:11.265][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-24 12:43:11.266][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-24 12:43:11.268][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-24 12:43:11.269][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-24 12:43:11.270][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-24 12:43:11.271][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-24 12:43:11.272][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-24 12:43:11.273][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-24 12:43:11.275][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-24 12:43:11.277][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-24 12:43:11.277][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-24 12:43:11.278][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.280][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.356][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[2024-06-24 12:43:11.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-24 12:43:11.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.373][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-24 12:43:11.375][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-24 12:43:11.377][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.379][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.380][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.381][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-24 12:43:11.382][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.383][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.384][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.385][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-24 12:43:11.386][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-24 12:43:11.387][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-24 12:43:11.388][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.388][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-24 12:43:11.389][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-24 12:43:11.391][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-24 12:43:11.392][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-24 12:43:11.393][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-24 12:43:11.393][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-24 12:43:11.393][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-24 12:43:11.393][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-24 12:43:11.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:11.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:11.396][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-24 12:43:11.397][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-24 12:43:11.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-24 12:43:11.398][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-24 12:43:11.399][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:11.399][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-24 12:43:11.400][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-24 12:43:11.401][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-24 12:43:11.401][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-24 12:43:11.402][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-24 12:43:11.402][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-24 12:43:11.403][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-24 12:43:11.405][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-24 12:43:11.407][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-24 12:43:11.409][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-24 12:43:11.411][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-24 12:43:11.413][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-24 12:43:11.417][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-24 12:43:11.418][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-24 12:43:11.419][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-24 12:43:11.420][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-24 12:43:11.421][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:11.422][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-24 12:43:11.423][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-24 12:43:11.424][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-24 12:43:11.426][biodb::testThat]
biodb.INFO [2024-06-24 12:43:11.427][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-06-24 12:43:11.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-24 12:43:11.428][biodb::testThat]
biodb.DEBUG[2024-06-24 12:43:11.431][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-24 12:43:11.435][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:11.436][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-24 12:43:11.438][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:11.439][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-24 12:43:11.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-24 12:43:11.454][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-24 12:43:11.456][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-06-24 12:43:11.457][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-24 12:43:11.458][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-06-24 12:43:11.463][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-06-24 12:43:11.464][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-24 12:43:11.466][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-06-24 12:43:11.467][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-24 12:43:11.468][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-24 12:43:11.469][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-24 12:43:11.470][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-24 12:43:11.471][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-24 12:43:11.472][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-24 12:43:11.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:11.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-24 12:43:11.486][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-06-24 12:43:11.489][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-24 12:43:11.490][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-24 12:43:11.491][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-06-24 12:43:11.571][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-06-24 12:43:11.707][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-24 12:43:11.710][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-06-24 12:43:11.714][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-06-24 12:43:11.717][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-06-24 12:43:11.719][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-24 12:43:11.720][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-24 12:43:11.721][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-24 12:43:11.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-24 12:43:11.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-24 12:43:11.737][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:11.738][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:11.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.740][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:11.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:11.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.745][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:11.746][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:11.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.748][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.750][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-24 12:43:11.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-24 12:43:11.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.754][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:11.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:11.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.756][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.758][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-24 12:43:11.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-24 12:43:11.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.761][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-24 12:43:11.762][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-24 12:43:11.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.763][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.765][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-24 12:43:11.766][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-24 12:43:11.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.767][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.768][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:11.769][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:11.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.771][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.772][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:11.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-24 12:43:11.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.775][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:11.776][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:11.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.778][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.779][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-24 12:43:11.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-24 12:43:11.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.783][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:11.784][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:11.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.785][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:11.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-24 12:43:11.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.791][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:11.792][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:11.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.794][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-24 12:43:11.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-24 12:43:11.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.800][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:11.801][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:11.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.803][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.804][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-24 12:43:11.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-24 12:43:11.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.808][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:11.808][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:11.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.810][ef$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.811][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-24 12:43:11.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-24 12:43:11.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:11.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:11.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:11.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:11.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:11.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:11.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-24 12:43:11.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-24 12:43:11.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:11.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:11.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:11.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:11.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:11.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:11.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:11.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:11.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:11.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:11.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-24 12:43:11.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-24 12:43:11.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-24 12:43:11.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-24 12:43:11.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-24 12:43:11.848][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-06-24 12:43:11.852][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-24 12:43:11.853][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-24 12:43:11.854][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-24 12:43:11.855][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-24 12:43:11.856][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-24 12:43:11.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-24 12:43:11.857][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-24 12:43:11.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-24 12:43:11.859][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-24 12:43:11.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
> 
> proc.time()
   user  system elapsed 
 17.542   1.092  24.608

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.4960.6713.348
ChebiEntry0.4190.0160.438